rs9572182

Variant names:

• chr13-69512198-T-C
• rs9572182
• ENST00000737773.1:n.131-20761T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-69512198-T-C
• chr13-69512198-T-G

Variant summary

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

The ENST00000737773.1(ENSG00000296278):​n.131-20761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,028 control chromosomes in the GnomAD database, including 17,378 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 0.47 (17378 hom., cov: 32)
• Consequence: ENSG00000296278 ENST00000737773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 publications found

Genes affected

ENSG00000296278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737773.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296278	ENST00000737773.1		n.131-20761T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72068 AN: 151910 Hom.: 17355 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.475 AC: 72140 AN: 152028 Hom.: 17378 Cov.: 32 AF XY: 0.474 AC XY: 35263 AN XY: 74320

African (AFR) AF: 0.433 AC: 17950 AN: 41464

American (AMR) AF: 0.407 AC: 6213 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2228 AN: 5146

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5074 AN: 10562

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35136 AN: 67976

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.492 Hom.: 51168

Bravo AF: 0.466

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9572182;

hg19: chr13-70086330;