rs2844682

Variant names:

• chr6-30978371-G-A
• rs2844682

Your query was ambiguous. Multiple possible variants found:

• chr6-30978371-G-A
• chr6-30978371-G-C
• chr6-30978371-G-T

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 0.147 in 152,094 control chromosomes in the GnomAD database, including 1,745 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 0.15 (1745 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.147 AC: 22389 AN: 151976 Hom.: 1737 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.147 AC: 22415 AN: 152094 Hom.: 1745 Cov.: 31 AF XY: 0.146 AC XY: 10820 AN XY: 74340

African (AFR) AF: 0.154 AC: 6407 AN: 41480

American (AMR) AF: 0.203 AC: 3095 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3464

East Asian (EAS) AF: 0.112 AC: 579 AN: 5174

South Asian (SAS) AF: 0.111 AC: 538 AN: 4828

European-Finnish (FIN) AF: 0.0878 AC: 929 AN: 10580

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9463 AN: 67982

Other (OTH) AF: 0.167 AC: 352 AN: 2112

Alfa AF: 0.146 Hom.: 4936

Bravo AF: 0.157

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.56
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2844682; hg19: chr6-30946148;