rs9356147

Variant names:

• chr6-163772381-A-G
• rs9356147
• ENST00000657138.1:n.163+12952A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-163772381-A-G
• chr6-163772381-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657138.1(ENSG00000235538):​n.163+12952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,050 control chromosomes in the GnomAD database, including 28,205 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 0.60 (28205 hom., cov: 32)
• Consequence: ENSG00000235538 ENST00000657138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

ENSG00000235538 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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
ENSG00000235538	ENST00000657138.1	n.163+12952A>G		intron_variant	Intron 1 of 1
ENSG00000235538	ENST00000657157.1	n.361-760A>G		intron_variant	Intron 3 of 3
ENSG00000235538	ENST00000657614.1	n.330-760A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91878 AN: 151934 Hom.: 28171 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.605 AC: 91957 AN: 152050 Hom.: 28205 Cov.: 32 AF XY: 0.606 AC XY: 45016 AN XY: 74336

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.616

Alfa AF: 0.623 Hom.: 24229

Bravo AF: 0.602

Asia WGS AF: 0.707 AC: 2457 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9356147; hg19: chr6-164193413; COSMIC: COSV69432400;