rs1958781

Variant names:

• chr14-49366783-C-A
• rs1958781

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 0.448 in 151,964 control chromosomes in the GnomAD database, including 15,843 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 0.45 (15843 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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: 0.448 AC: 67955 AN: 151850 Hom.: 15826 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.448 AC: 68012 AN: 151964 Hom.: 15843 Cov.: 31 AF XY: 0.440 AC XY: 32679 AN XY: 74282

African (AFR) AF: 0.482 AC: 19979 AN: 41418

American (AMR) AF: 0.449 AC: 6858 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1551 AN: 3464

East Asian (EAS) AF: 0.00694 AC: 36 AN: 5184

South Asian (SAS) AF: 0.227 AC: 1090 AN: 4812

European-Finnish (FIN) AF: 0.464 AC: 4898 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32030 AN: 67940

Other (OTH) AF: 0.439 AC: 927 AN: 2112

Alfa AF: 0.465 Hom.: 10607

Bravo AF: 0.449

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.31
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1958781; hg19: chr14-49833501;