rs1246182

Variant names:

• chr6-156648182-G-A
• rs1246182
• ENST00000743650.1:n.372-14395C>T

Variant summary

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

The ENST00000743650.1(ENSG00000296922):​n.372-14395C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,012 control chromosomes in the GnomAD database, including 25,222 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 0.57 (25222 hom., cov: 31)
• Consequence: ENSG00000296922 ENST00000743650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 5 publications found

Genes affected

ENSG00000296922 (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 = 0.73 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
ENSG00000296922	ENST00000743650.1	n.372-14395C>T		intron_variant	Intron 3 of 3
ENSG00000296922	ENST00000743651.1	n.369-14395C>T		intron_variant	Intron 2 of 2
ENSG00000296922	ENST00000743652.1	n.282-14395C>T		intron_variant	Intron 2 of 2
ENSG00000296922	ENST00000743653.1	n.149+11995C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87251 AN: 151894 Hom.: 25186 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.575 AC: 87340 AN: 152012 Hom.: 25222 Cov.: 31 AF XY: 0.578 AC XY: 42938 AN XY: 74276

African (AFR) AF: 0.551 AC: 22834 AN: 41464

American (AMR) AF: 0.626 AC: 9577 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2041 AN: 3466

East Asian (EAS) AF: 0.658 AC: 3404 AN: 5176

South Asian (SAS) AF: 0.751 AC: 3613 AN: 4812

European-Finnish (FIN) AF: 0.549 AC: 5776 AN: 10516

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38245 AN: 67978

Other (OTH) AF: 0.575 AC: 1210 AN: 2106

Alfa AF: 0.576 Hom.: 27332

Bravo AF: 0.582

Asia WGS AF: 0.653 AC: 2268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.77
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1246182; hg19: chr6-156969316; COSMIC: COSV69431341;