chr6-163772381-A-G

Variant names:

• chr6-163772381-A-G
• rs9356147
• ENST00000657138.2:n.389+12952A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657138.2(ENSG00000235538):​n.389+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 ENST00000657138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 3 publications found

Genes affected

ENSG00000235538 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657138.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235538	ENST00000657138.2		n.389+12952A>G		intron	N/A
	ENSG00000235538	ENST00000657157.2		n.375-760A>G		intron	N/A
	ENSG00000235538	ENST00000657614.1		n.330-760A>G		intron	N/A

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

African (AFR) AF: 0.512 AC: 21221 AN: 41430

American (AMR) AF: 0.674 AC: 10303 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1963 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3612 AN: 5178

South Asian (SAS) AF: 0.698 AC: 3366 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6394 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.633 AC: 43068 AN: 67990

Other (OTH) AF: 0.616 AC: 1303 AN: 2114

Alfa AF: 0.623 Hom.: 28917

Bravo AF: 0.602

Asia WGS AF: 0.707 AC: 2457 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		0.19

Splicing

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

Other links and lift over

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