6-159852667-G-T

Variant names:

• chr6-159852667-G-T
• rs9457743
• ENST00000817607.1:n.148-1670G>T

Variant summary

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

The ENST00000817607.1(ENSG00000306392):​n.148-1670G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,006 control chromosomes in the GnomAD database, including 31,320 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 0.64 (31320 hom., cov: 31)
• Consequence: ENSG00000306392 ENST00000817607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 7 publications found

Genes affected

ENSG00000306392 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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
ENSG00000306392	ENST00000817607.1	n.148-1670G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96967 AN: 151888 Hom.: 31313 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.638 AC: 97002 AN: 152006 Hom.: 31320 Cov.: 31 AF XY: 0.630 AC XY: 46825 AN XY: 74288

African (AFR) AF: 0.633 AC: 26235 AN: 41478

American (AMR) AF: 0.598 AC: 9127 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2316 AN: 3468

East Asian (EAS) AF: 0.341 AC: 1762 AN: 5164

South Asian (SAS) AF: 0.647 AC: 3110 AN: 4804

European-Finnish (FIN) AF: 0.582 AC: 6132 AN: 10542

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46214 AN: 67976

Other (OTH) AF: 0.657 AC: 1383 AN: 2106

Alfa AF: 0.654 Hom.: 15185

Bravo AF: 0.637

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.55
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9457743; hg19: chr6-160273699;