rs7336380

Variant names:

• chr13-37613611-G-A
• rs7336380
• ENST00000744989.1:n.49-14415G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-37613611-G-A
• chr13-37613611-G-C

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.49-14415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,020 control chromosomes in the GnomAD database, including 43,905 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 0.75 (43905 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 publications found

Genes affected

ENSG00000297050 (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 (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744989.1. 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
	ENSG00000297050	ENST00000744989.1		n.49-14415G>A		intron	N/A
	ENSG00000297050	ENST00000744990.1		n.71-14415G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114583 AN: 151902 Hom.: 43877 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.754 AC: 114663 AN: 152020 Hom.: 43905 Cov.: 32 AF XY: 0.746 AC XY: 55389 AN XY: 74286

African (AFR) AF: 0.728 AC: 30183 AN: 41456

American (AMR) AF: 0.728 AC: 11115 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2933 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1619 AN: 5142

South Asian (SAS) AF: 0.701 AC: 3385 AN: 4828

European-Finnish (FIN) AF: 0.756 AC: 7981 AN: 10562

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54780 AN: 67980

Other (OTH) AF: 0.775 AC: 1637 AN: 2112

Alfa AF: 0.786 Hom.: 9802

Bravo AF: 0.751

Asia WGS AF: 0.556 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		-0.54

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: rs7336380;

hg19: chr13-38187748;