rs926938

Positions:

• chr1-114697195-A-G
• chr1-114697195-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.523 in 151,986 control chromosomes in the GnomAD database, including 21,074 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 0.52 (21074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79401 AN: 151868 Hom.: 21061 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.523 AC: 79457 AN: 151986 Hom.: 21074 Cov.: 32 AF XY: 0.524 AC XY: 38955 AN XY: 74272

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.498

Alfa AF: 0.500 Hom.: 29762

Bravo AF: 0.526

Asia WGS AF: 0.605 AC: 2103 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	2.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926938; hg19: chr1-115239816;