chr6-415406-A-G

Variant names:

• chr6-415406-A-G
• rs9503644

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 0.799 in 152,084 control chromosomes in the GnomAD database, including 48,933 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 0.80 (48933 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121378 AN: 151966 Hom.: 48907 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.799 AC: 121459 AN: 152084 Hom.: 48933 Cov.: 31 AF XY: 0.799 AC XY: 59367 AN XY: 74338

African (AFR) AF: 0.692 AC: 28685 AN: 41458

American (AMR) AF: 0.816 AC: 12467 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2999 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3806 AN: 5170

South Asian (SAS) AF: 0.896 AC: 4326 AN: 4828

European-Finnish (FIN) AF: 0.800 AC: 8455 AN: 10570

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58110 AN: 67992

Other (OTH) AF: 0.798 AC: 1684 AN: 2110

Alfa AF: 0.828 Hom.: 15641

Bravo AF: 0.791

Asia WGS AF: 0.790 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.21
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs9503644; hg19: chr6-415406;