6-40388442-T-G

Variant names:

• chr6-40388442-T-G
• rs9462616

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 0.864 in 152,204 control chromosomes in the GnomAD database, including 57,004 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 0.86 (57004 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 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: 0.864 AC: 131400 AN: 152086 Hom.: 56968 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.864 AC: 131489 AN: 152204 Hom.: 57004 Cov.: 33 AF XY: 0.859 AC XY: 63896 AN XY: 74402

African (AFR) AF: 0.853 AC: 35393 AN: 41512

American (AMR) AF: 0.847 AC: 12964 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3184 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3610 AN: 5160

South Asian (SAS) AF: 0.870 AC: 4194 AN: 4822

European-Finnish (FIN) AF: 0.792 AC: 8395 AN: 10600

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60886 AN: 68020

Other (OTH) AF: 0.881 AC: 1862 AN: 2114

Alfa AF: 0.884 Hom.: 33338

Bravo AF: 0.864

Asia WGS AF: 0.792 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9462616; hg19: chr6-40356181;