rs13137776

Variant names:

• chr4-11463351-A-G
• rs13137776
• ENST00000662830.1:n.313-1050A>G

Variant summary

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

The ENST00000662830.1(ENSG00000287778):​n.313-1050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,030 control chromosomes in the GnomAD database, including 6,263 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 0.26 (6263 hom., cov: 31)
• Consequence: ENSG00000287778 ENST00000662830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 3 publications found

Genes affected

ENSG00000287778 (HGNC:58736):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662830.1. 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
	ENSG00000287778	ENST00000662830.1		n.313-1050A>G		intron	N/A
	ENSG00000287778	ENST00000835462.1		n.538-1050A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38947 AN: 151912 Hom.: 6252 Cov.: 31

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.256 AC: 38973 AN: 152030 Hom.: 6263 Cov.: 31 AF XY: 0.262 AC XY: 19494 AN XY: 74296

African (AFR) AF: 0.0653 AC: 2708 AN: 41488

American (AMR) AF: 0.263 AC: 4024 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2367 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4045 AN: 10556

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22098 AN: 67958

Other (OTH) AF: 0.265 AC: 556 AN: 2102

Alfa AF: 0.298 Hom.: 19918

Bravo AF: 0.238

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs13137776; hg19: chr4-11464975;