rs1324713

Variant names:

• chr1-195407805-C-T
• rs1324713

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 0.619 in 151,886 control chromosomes in the GnomAD database, including 30,005 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 0.62 (30005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 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: 0.619 AC: 93946 AN: 151768 Hom.: 29974 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.619 AC: 94028 AN: 151886 Hom.: 30005 Cov.: 32 AF XY: 0.615 AC XY: 45671 AN XY: 74212

African (AFR) AF: 0.495 AC: 20497 AN: 41422

American (AMR) AF: 0.634 AC: 9661 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2073 AN: 3464

East Asian (EAS) AF: 0.389 AC: 2013 AN: 5172

South Asian (SAS) AF: 0.534 AC: 2577 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6624 AN: 10524

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.713 AC: 48440 AN: 67932

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.647 Hom.: 5781

Bravo AF: 0.613

Asia WGS AF: 0.464 AC: 1613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1324713; hg19: chr1-195376935; COSMIC: COSV60010621;