6-44626422-T-G

Variant names:

• chr6-44626422-T-G
• rs556621

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 0.719 in 151,836 control chromosomes in the GnomAD database, including 40,326 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 0.72 (40326 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 29 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 (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.719 AC: 109098 AN: 151718 Hom.: 40288 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.719 AC: 109196 AN: 151836 Hom.: 40326 Cov.: 31 AF XY: 0.713 AC XY: 52882 AN XY: 74168

African (AFR) AF: 0.886 AC: 36682 AN: 41408

American (AMR) AF: 0.625 AC: 9540 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2318 AN: 3464

East Asian (EAS) AF: 0.493 AC: 2516 AN: 5104

South Asian (SAS) AF: 0.679 AC: 3272 AN: 4816

European-Finnish (FIN) AF: 0.615 AC: 6458 AN: 10506

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45925 AN: 67958

Other (OTH) AF: 0.727 AC: 1533 AN: 2110

Alfa AF: 0.682 Hom.: 153077

Bravo AF: 0.722

Asia WGS AF: 0.622 AC: 2164 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	1.9
DANN	Benign	0.34
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs556621; hg19: chr6-44594159;