6-44626422-T-G

Position:

• chr6-44626422-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.727

Alfa AF: 0.675 Hom.: 68008

Bravo AF: 0.722

Asia WGS AF: 0.622 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs556621; hg19: chr6-44594159;