rs2811276

Variant names:

• chr1-178704778-T-C
• rs2811276

Your query was ambiguous. Multiple possible variants found:

• chr1-178704778-T-C
• chr1-178704778-T-G

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 0.293 in 152,078 control chromosomes in the GnomAD database, including 7,378 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 0.29 (7378 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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: 0.293 AC: 44526 AN: 151960 Hom.: 7379 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.293 AC: 44536 AN: 152078 Hom.: 7378 Cov.: 33 AF XY: 0.294 AC XY: 21851 AN XY: 74348

African (AFR) AF: 0.141 AC: 5848 AN: 41436

American (AMR) AF: 0.261 AC: 3986 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1497 AN: 5166

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4457 AN: 10590

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25141 AN: 67996

Other (OTH) AF: 0.317 AC: 668 AN: 2108

Alfa AF: 0.339 Hom.: 6088

Bravo AF: 0.274

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.62
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2811276; hg19: chr1-178673913;