rs9397738

Variant names:

• chr6-154665530-G-A
• rs9397738

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 0.871 in 152,170 control chromosomes in the GnomAD database, including 57,868 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 0.87 (57868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.908 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: 0.871 AC: 132407 AN: 152050 Hom.: 57810 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.871 AC: 132525 AN: 152170 Hom.: 57868 Cov.: 32 AF XY: 0.870 AC XY: 64730 AN XY: 74378

African (AFR) AF: 0.916 AC: 38055 AN: 41538

American (AMR) AF: 0.895 AC: 13683 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2927 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4111 AN: 5172

South Asian (SAS) AF: 0.738 AC: 3551 AN: 4812

European-Finnish (FIN) AF: 0.877 AC: 9278 AN: 10574

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58111 AN: 68010

Other (OTH) AF: 0.872 AC: 1838 AN: 2108

Alfa AF: 0.859 Hom.: 203901

Bravo AF: 0.877

Asia WGS AF: 0.809 AC: 2806 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.039
DANN	Benign	0.64
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9397738; hg19: chr6-154986664;