rs1979255

Variant names:

• chr4-189396926-C-G
• rs1979255

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.64 in 152,022 control chromosomes in the GnomAD database, including 31,314 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 0.64 (31314 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97190 AN: 151904 Hom.: 31296 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.640 AC: 97251 AN: 152022 Hom.: 31314 Cov.: 33 AF XY: 0.634 AC XY: 47117 AN XY: 74312

African (AFR) AF: 0.673 AC: 27897 AN: 41468

American (AMR) AF: 0.581 AC: 8863 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2873 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2893 AN: 4832

European-Finnish (FIN) AF: 0.547 AC: 5771 AN: 10550

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.652 AC: 44342 AN: 67980

Other (OTH) AF: 0.657 AC: 1379 AN: 2098

Alfa AF: 0.639 Hom.: 3897

Bravo AF: 0.644

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.35
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1979255; hg19: chr4-190318080; COSMIC: COSV50192825;