chr6-30978719-T-G

Variant names:

• chr6-30978719-T-G
• rs2844680

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 0.568 in 151,954 control chromosomes in the GnomAD database, including 24,652 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 0.57 (24652 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.573 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: 0.568 AC: 86217 AN: 151836 Hom.: 24645 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.568 AC: 86264 AN: 151954 Hom.: 24652 Cov.: 31 AF XY: 0.559 AC XY: 41479 AN XY: 74264

African (AFR) AF: 0.575 AC: 23834 AN: 41430

American (AMR) AF: 0.582 AC: 8892 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3466

East Asian (EAS) AF: 0.518 AC: 2667 AN: 5152

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4818

European-Finnish (FIN) AF: 0.464 AC: 4891 AN: 10546

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39283 AN: 67940

Other (OTH) AF: 0.588 AC: 1240 AN: 2110

Alfa AF: 0.579 Hom.: 35743

Bravo AF: 0.583

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2844680; hg19: chr6-30946496;