rs4750012

Variant names:

• chr10-6135831-C-T
• rs4750012
• ENST00000841432.1:n.621+5187G>A

Variant summary

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

The ENST00000841432.1(ENSG00000309490):​n.621+5187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,842 control chromosomes in the GnomAD database, including 14,190 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 0.43 (14190 hom., cov: 32)
• Consequence: ENSG00000309490 ENST00000841432.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 4 publications found

Genes affected

ENSG00000309490 (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 (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841432.1. 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
	ENSG00000309490	ENST00000841432.1		n.621+5187G>A		intron	N/A
	ENSG00000309490	ENST00000841433.1		n.618+5187G>A		intron	N/A
	ENSG00000309490	ENST00000841434.1		n.752+5034G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65284 AN: 151724 Hom.: 14178 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.430 AC: 65338 AN: 151842 Hom.: 14190 Cov.: 32 AF XY: 0.428 AC XY: 31755 AN XY: 74190

African (AFR) AF: 0.389 AC: 16124 AN: 41404

American (AMR) AF: 0.476 AC: 7256 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5164

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4824

European-Finnish (FIN) AF: 0.410 AC: 4301 AN: 10498

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30311 AN: 67914

Other (OTH) AF: 0.473 AC: 998 AN: 2108

Alfa AF: 0.441 Hom.: 7090

Bravo AF: 0.437

Asia WGS AF: 0.371 AC: 1293 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	9.8
DANN	Benign	0.85
PhyloP100		-0.48

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: rs4750012;

hg19: chr10-6177794;