rs2796267

Variant names:

• chr1-207751561-G-A
• rs2796267
• ENST00000830828.1:n.388C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000830828.1(ENSG00000308069):​n.388C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000308069 ENST00000830828.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.27
• Publications: 32 publications found

Genes affected

ENSG00000308069 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId is 1280415.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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
ENSG00000308069	ENST00000830828.1	n.388C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308069	ENST00000830829.1	n.207C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308069	ENST00000830830.1	n.268C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308069	ENST00000830831.1	n.362C>T		non_coding_transcript_exon_variant	Exon 1 of 2

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

African (AFR) AF: 0.700 AC: 28919 AN: 41314

American (AMR) AF: 0.506 AC: 7721 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3220 AN: 5118

South Asian (SAS) AF: 0.565 AC: 2696 AN: 4772

European-Finnish (FIN) AF: 0.511 AC: 5371 AN: 10512

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41370 AN: 67860

Other (OTH) AF: 0.649 AC: 1364 AN: 2102

Alfa AF: 0.609 Hom.: 13371

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
PhyloP100		-3.3
PromoterAI		-0.0040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2796267; hg19: chr1-207924906;