rs9296538

Variant names:

• chr6-47226713-A-T
• rs9296538

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 0.414 in 152,034 control chromosomes in the GnomAD database, including 14,475 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 0.41 (14475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 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: 0.415 AC: 62983 AN: 151916 Hom.: 14460 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.414 AC: 63018 AN: 152034 Hom.: 14475 Cov.: 32 AF XY: 0.410 AC XY: 30502 AN XY: 74306

African (AFR) AF: 0.225 AC: 9326 AN: 41480

American (AMR) AF: 0.381 AC: 5823 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1600 AN: 5162

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5016 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36383 AN: 67960

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.472 Hom.: 2271

Bravo AF: 0.392

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9296538; hg19: chr6-47194449;