6-30501413-C-T

Variant names:

• chr6-30501413-C-T
• rs2844724

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 152,076 control chromosomes in the GnomAD database, including 36,719 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 (36719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	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: 105338 AN: 151958 Hom.: 36679 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.693 AC: 105425 AN: 152076 Hom.: 36719 Cov.: 32 AF XY: 0.691 AC XY: 51341 AN XY: 74324

African (AFR) AF: 0.770 AC: 31955 AN: 41500

American (AMR) AF: 0.616 AC: 9410 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2815 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3361 AN: 5176

South Asian (SAS) AF: 0.761 AC: 3668 AN: 4820

European-Finnish (FIN) AF: 0.673 AC: 7107 AN: 10554

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.659 AC: 44767 AN: 67978

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.671 Hom.: 84079

Bravo AF: 0.693

Asia WGS AF: 0.678 AC: 2361 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	0.69
DANN	Benign	0.19
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs2844724; hg19: chr6-30469190;