chr4-2570552-C-T

Variant names:

• chr4-2570552-C-T
• rs707341
• NM_001366318.2:c.256-25532C>T

Variant summary

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

The NM_001366318.2(FAM193A):​c.256-25532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,194 control chromosomes in the GnomAD database, including 115 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 0.030 (115 hom., cov: 31)
• Consequence: FAM193A NM_001366318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 publications found

Genes affected

FAM193A (HGNC:16822): (family with sequence similarity 193 member A)

ENSG00000290180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0305 (4639/152194) while in subpopulation NFE AF = 0.0429 (2916/67984). AF 95% confidence interval is 0.0416. There are 115 homozygotes in GnomAd4. There are 2324 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 115 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366318.2. 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
	FAM193A	NM_001366318.2	MANE Select	c.256-25532C>T		intron	N/A	NP_001353247.1
	FAM193A	NM_001366316.2		c.85-25532C>T		intron	N/A	NP_001353245.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM193A	ENST00000637812.2	TSL:5 MANE Select	c.256-25532C>T		intron	N/A	ENSP00000490564.1
	ENSG00000290180	ENST00000703446.1		n.297-25532C>T		intron	N/A	ENSP00000515299.1

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4642 AN: 152076 Hom.: 115 Cov.: 31

Gnomad AFR AF: 0.00681

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0305 AC: 4639 AN: 152194 Hom.: 115 Cov.: 31 AF XY: 0.0312 AC XY: 2324 AN XY: 74402

African (AFR) AF: 0.00679 AC: 282 AN: 41538

American (AMR) AF: 0.0285 AC: 436 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00477 AC: 23 AN: 4826

European-Finnish (FIN) AF: 0.0703 AC: 743 AN: 10576

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0429 AC: 2916 AN: 67984

Other (OTH) AF: 0.0313 AC: 66 AN: 2106

Alfa AF: 0.0404 Hom.: 205

Bravo AF: 0.0257

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.30
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs707341; hg19: chr4-2572279;