3-115514065-T-C

Variant names:

• chr3-115514065-T-C
• rs10511343
• ENST00000657371.1:n.593-50121T>C

Variant summary

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

The ENST00000657371.1(ENSG00000242880):​n.593-50121T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,044 control chromosomes in the GnomAD database, including 18,115 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 0.48 (18115 hom., cov: 33)
• Consequence: ENSG00000242880 ENST00000657371.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 5 publications found

Genes affected

ENSG00000242880 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 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
ENSG00000242880	ENST00000657371.1	n.593-50121T>C		intron_variant	Intron 5 of 5
ENSG00000242880	ENST00000662602.1	n.818-50121T>C		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73505 AN: 151924 Hom.: 18086 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.484 AC: 73572 AN: 152044 Hom.: 18115 Cov.: 33 AF XY: 0.489 AC XY: 36361 AN XY: 74322

African (AFR) AF: 0.381 AC: 15790 AN: 41464

American (AMR) AF: 0.557 AC: 8507 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1943 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2891 AN: 5174

South Asian (SAS) AF: 0.586 AC: 2825 AN: 4822

European-Finnish (FIN) AF: 0.560 AC: 5919 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34168 AN: 67962

Other (OTH) AF: 0.499 AC: 1054 AN: 2114

Alfa AF: 0.500 Hom.: 79429

Bravo AF: 0.480

Asia WGS AF: 0.576 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10511343; hg19: chr3-115232912;