rs2796267

Positions:

• chr1-207751561-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 23, 2021

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;