6-30371825-T-C

Variant names:

• chr6-30371825-T-C
• rs2844746

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 0.693 in 151,926 control chromosomes in the GnomAD database, including 36,914 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 0.69 (36914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105127 AN: 151808 Hom.: 36880 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.693 AC: 105214 AN: 151926 Hom.: 36914 Cov.: 32 AF XY: 0.693 AC XY: 51444 AN XY: 74282

African (AFR) AF: 0.782 AC: 32407 AN: 41438

American (AMR) AF: 0.657 AC: 10029 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2369 AN: 3464

East Asian (EAS) AF: 0.874 AC: 4530 AN: 5184

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7480 AN: 10536

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43141 AN: 67898

Other (OTH) AF: 0.658 AC: 1390 AN: 2112

Alfa AF: 0.659 Hom.: 126125

Bravo AF: 0.693

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.21
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2844746; hg19: chr6-30339602;