1-114697195-A-G

Variant names:

• chr1-114697195-A-G
• rs926938

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 0.523 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
• Publications: 17 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 (SAS) allele frequency at 95% confidence interval = 0.606 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: 0.523 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

African (AFR) AF: 0.541 AC: 22434 AN: 41438

American (AMR) AF: 0.574 AC: 8770 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1480 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2662 AN: 5152

South Asian (SAS) AF: 0.624 AC: 3011 AN: 4822

European-Finnish (FIN) AF: 0.509 AC: 5369 AN: 10542

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34104 AN: 67960

Other (OTH) AF: 0.498 AC: 1048 AN: 2106

Alfa AF: 0.507 Hom.: 74159

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs926938; hg19: chr1-115239816;