rs9394438

Variant names:

• chr6-37564327-G-A
• rs9394438

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 0.31 in 152,040 control chromosomes in the GnomAD database, including 8,283 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 0.31 (8283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.310 AC: 47135 AN: 151922 Hom.: 8263 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.310 AC: 47182 AN: 152040 Hom.: 8283 Cov.: 32 AF XY: 0.320 AC XY: 23795 AN XY: 74338

African (AFR) AF: 0.194 AC: 8063 AN: 41462

American (AMR) AF: 0.287 AC: 4393 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3466

East Asian (EAS) AF: 0.706 AC: 3647 AN: 5168

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4814

European-Finnish (FIN) AF: 0.473 AC: 5001 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22579 AN: 67958

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.322 Hom.: 35326

Bravo AF: 0.293

Asia WGS AF: 0.558 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9394438; hg19: chr6-37532103;