rs2796267

Variant names:

• chr1-207751561-G-A
• rs2796267

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.619 in 151,598 control chromosomes in the GnomAD database, including 29,370 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.62 (29370 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.27

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-207751561-G-A is Benign according to our data. Variant chr1-207751561-G-A is described in ClinVar as [Benign]. Clinvar id is 1280415.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-207751561-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.618 AC: 93670 AN: 151480 Hom.: 29318 Cov.: 28

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.619 AC: 93768 AN: 151598 Hom.: 29370 Cov.: 28 AF XY: 0.612 AC XY: 45287 AN XY: 74038

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.649

Alfa AF: 0.610 Hom.: 11981

Bravo AF: 0.619

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 23, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 32869896) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2796267; hg19: chr1-207924906;