3-58870245-G-A

Variant names:

• chr3-58870245-G-A
• rs77036152
• NM_001394063.1:c.780C>T

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BS1 BS2

The NM_001351532.2(CFAP20DC):​c.-162C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00217 in 1,613,766 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.010 (31 hom., cov: 32)
  • Exomes 𝑓: 0.0013 (25 hom.)
• Consequence: CFAP20DC NM_001351532.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.155
• Publications: 1 publications found

Genes affected

CFAP20DC (HGNC:24763): (CFAP20 domain containing)

CFAP20DC-AS1 (HGNC:41063): (CFAP20DC antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP6: Variant 3-58870245-G-A is Benign according to our data. Variant chr3-58870245-G-A is described in ClinVar as Benign. ClinVar VariationId is 770534.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0101 (1537/152228) while in subpopulation AFR AF = 0.0342 (1421/41518). AF 95% confidence interval is 0.0327. There are 31 homozygotes in GnomAd4. There are 725 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351532.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC	NM_001394063.1	MANE Select	c.780C>T	p.Ile260Ile	synonymous	Exon 8 of 17	NP_001380992.1	A0A2U3TZK7
	CFAP20DC	NM_001351532.2		c.-162C>T		5_prime_UTR_premature_start_codon_gain	Exon 8 of 15	NP_001338461.1
	CFAP20DC	NM_001351530.2		c.615C>T	p.Ile205Ile	synonymous	Exon 7 of 16	NP_001338459.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC	ENST00000482387.7	TSL:5 MANE Select	c.780C>T	p.Ile260Ile	synonymous	Exon 8 of 17	ENSP00000417122.2	A0A2U3TZK7
	CFAP20DC	ENST00000468415.6	TSL:1	n.*199C>T		non_coding_transcript_exon	Exon 8 of 15	ENSP00000419142.2	F8WF72
	CFAP20DC	ENST00000468415.6	TSL:1	n.*199C>T		3_prime_UTR	Exon 8 of 15	ENSP00000419142.2	F8WF72

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1535 AN: 152110 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00360

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.0110

GnomAD2 exomes AF: 0.00307 AC: 773 AN: 251460 AF XY: 0.00256

Gnomad AFR exome AF: 0.0342

Gnomad AMR exome AF: 0.00301

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000791

Gnomad OTH exome AF: 0.00228

GnomAD4 exome AF: 0.00135 AC: 1971 AN: 1461538 Hom.: 25 Cov.: 31 AF XY: 0.00126 AC XY: 919 AN XY: 727116

African (AFR) AF: 0.0331 AC: 1107 AN: 33476

American (AMR) AF: 0.00311 AC: 139 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.000325 AC: 28 AN: 86254

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53420

Middle Eastern (MID) AF: 0.00641 AC: 37 AN: 5768

European-Non Finnish (NFE) AF: 0.000430 AC: 478 AN: 1111680

Other (OTH) AF: 0.00300 AC: 181 AN: 60386

GnomAD4 genome AF: 0.0101 AC: 1537 AN: 152228 Hom.: 31 Cov.: 32 AF XY: 0.00974 AC XY: 725 AN XY: 74432

African (AFR) AF: 0.0342 AC: 1421 AN: 41518

American (AMR) AF: 0.00359 AC: 55 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000529 AC: 36 AN: 68014

Other (OTH) AF: 0.0109 AC: 23 AN: 2114

Alfa AF: 0.00416 Hom.: 9

Bravo AF: 0.0116

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.000818

EpiControl AF: 0.00130

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	4.1
DANN	Benign	0.83
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs77036152; hg19: chr3-58855971;