rs2796268

Positions:

• chr1-207751847-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 0.583 in 152,076 control chromosomes in the GnomAD database, including 26,379 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (26379 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 1-207751847-G-A is Benign according to our data. Variant chr1-207751847-G-A is described in ClinVar as [Benign]. Clinvar id is 1247101.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-207751847-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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: 0.583 AC: 88662 AN: 151960 Hom.: 26364 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.583 AC: 88710 AN: 152076 Hom.: 26379 Cov.: 33 AF XY: 0.584 AC XY: 43412 AN XY: 74364

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.643

Alfa AF: 0.587 Hom.: 3539

Bravo AF: 0.575

Asia WGS AF: 0.769 AC: 2672 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

Nov 10, 2018

This variant is associated with the following publications: (PMID: 15661753) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2796268; hg19: chr1-207925192;