rs13137776

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287778	ENST00000662830.1	n.313-1050A>G		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.0653

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.265

Alfa AF: 0.315 Hom.: 12752

Bravo AF: 0.238

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13137776; hg19: chr4-11464975;