6-103463699-T-A

Variant names:

• chr6-103463699-T-A
• rs9322729

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 0.317 in 151,752 control chromosomes in the GnomAD database, including 8,332 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 0.32 (8332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.317 AC: 48051 AN: 151634 Hom.: 8294 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.317 AC: 48140 AN: 151752 Hom.: 8332 Cov.: 32 AF XY: 0.319 AC XY: 23634 AN XY: 74162

African (AFR) AF: 0.463 AC: 19163 AN: 41404

American (AMR) AF: 0.341 AC: 5173 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1803 AN: 5114

South Asian (SAS) AF: 0.205 AC: 988 AN: 4828

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10576

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16536 AN: 67886

Other (OTH) AF: 0.274 AC: 578 AN: 2110

Alfa AF: 0.134 Hom.: 230

Bravo AF: 0.334

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.27
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs9322729; hg19: chr6-103911574;