chr20-7125573-A-C

Variant names:

• chr20-7125573-A-C
• rs17808497
• ENST00000425900.1:n.82-20784A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000425900.1(ENSG00000232271):​n.82-20784A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,200 control chromosomes in the GnomAD database, including 122 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.035 (122 hom., cov: 31)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 2 publications found

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0355 (5400/152200) while in subpopulation NFE AF = 0.0424 (2885/68008). AF 95% confidence interval is 0.0411. There are 122 homozygotes in GnomAd4. There are 2618 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 122 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232271	ENST00000425900.1	TSL:2	n.82-20784A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5390 AN: 152082 Hom.: 122 Cov.: 31

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0498

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0355 AC: 5400 AN: 152200 Hom.: 122 Cov.: 31 AF XY: 0.0352 AC XY: 2618 AN XY: 74432

African (AFR) AF: 0.0243 AC: 1010 AN: 41516

American (AMR) AF: 0.0291 AC: 445 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0802 AC: 278 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00704 AC: 34 AN: 4832

European-Finnish (FIN) AF: 0.0540 AC: 573 AN: 10616

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0424 AC: 2885 AN: 68008

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0389 Hom.: 21

Bravo AF: 0.0340

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.78
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17808497; hg19: chr20-7106220;