11-130477295-G-T

Variant names:

• chr11-130477295-G-T
• rs4937523
• ENST00000777947.1:n.93+507G>T

Variant summary

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

The ENST00000777947.1(ENSG00000301321):​n.93+507G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,044 control chromosomes in the GnomAD database, including 11,807 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 0.38 (11807 hom., cov: 32)
• Consequence: ENSG00000301321 ENST00000777947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 5 publications found

Genes affected

ENSG00000301321 (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 (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777947.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301321	ENST00000777947.1		n.93+507G>T		intron	N/A
	ENSG00000301321	ENST00000777948.1		n.303+268G>T		intron	N/A
	ENSG00000301321	ENST00000777949.1		n.236+268G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58333 AN: 151926 Hom.: 11787 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.384 AC: 58402 AN: 152044 Hom.: 11807 Cov.: 32 AF XY: 0.387 AC XY: 28749 AN XY: 74300

African (AFR) AF: 0.509 AC: 21087 AN: 41454

American (AMR) AF: 0.357 AC: 5452 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2478 AN: 5148

South Asian (SAS) AF: 0.418 AC: 2014 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3817 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21085 AN: 67980

Other (OTH) AF: 0.386 AC: 814 AN: 2110

Alfa AF: 0.337 Hom.: 37877

Bravo AF: 0.389

Asia WGS AF: 0.451 AC: 1563 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	1.8
DANN	Benign	0.55
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs4937523; hg19: chr11-130347190;