rs13072940

Variant names:

• chr3-36801132-T-A
• rs13072940
• ENST00000753312.1:n.81+11146A>T

Variant summary

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

The ENST00000753312.1(ENSG00000292977):​n.81+11146A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,038 control chromosomes in the GnomAD database, including 10,518 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 0.36 (10518 hom., cov: 32)
• Consequence: ENSG00000292977 ENST00000753312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 9 publications found

Genes affected

ENSG00000292977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753312.1. 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
	ENSG00000292977	ENST00000753312.1		n.81+11146A>T		intron	N/A
	ENSG00000292977	ENST00000753313.1		n.79+11146A>T		intron	N/A
	ENSG00000292977	ENST00000753314.1		n.76+11146A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55393 AN: 151918 Hom.: 10522 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.364 AC: 55413 AN: 152038 Hom.: 10518 Cov.: 32 AF XY: 0.364 AC XY: 27072 AN XY: 74314

African (AFR) AF: 0.380 AC: 15777 AN: 41478

American (AMR) AF: 0.263 AC: 4018 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5180

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4820

European-Finnish (FIN) AF: 0.453 AC: 4782 AN: 10546

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26373 AN: 67958

Other (OTH) AF: 0.368 AC: 778 AN: 2114

Alfa AF: 0.389 Hom.: 1486

Bravo AF: 0.350

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.8
DANN	Benign	0.88
PhyloP100		0.033

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: rs13072940;

hg19: chr3-36842623;