chr6-14752642-C-T

Variant names:

• chr6-14752642-C-T
• rs4712240
• ENST00000629853.3:n.313+37348G>A

Variant summary

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

The ENST00000629853.3(ENSG00000234261):​n.313+37348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,084 control chromosomes in the GnomAD database, including 58,210 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 0.87 (58210 hom., cov: 31)
• Consequence: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 1 publications found

Genes affected

ENSG00000234261 (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 (EAS) allele frequency at 95% confidence interval = 0.949 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
ENSG00000234261	ENST00000629853.3	n.313+37348G>A		intron_variant	Intron 3 of 3	5
ENSG00000234261	ENST00000689305.1	n.179-11591G>A		intron_variant	Intron 1 of 2
ENSG00000234261	ENST00000702363.1	n.187-21164G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132677 AN: 151966 Hom.: 58179 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.873 AC: 132756 AN: 152084 Hom.: 58210 Cov.: 31 AF XY: 0.875 AC XY: 65010 AN XY: 74338

African (AFR) AF: 0.787 AC: 32617 AN: 41450

American (AMR) AF: 0.870 AC: 13286 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3261 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5019 AN: 5168

South Asian (SAS) AF: 0.913 AC: 4405 AN: 4826

European-Finnish (FIN) AF: 0.911 AC: 9625 AN: 10564

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61634 AN: 68024

Other (OTH) AF: 0.885 AC: 1863 AN: 2104

Alfa AF: 0.895 Hom.: 30338

Bravo AF: 0.863

Asia WGS AF: 0.921 AC: 3202 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	6.6
DANN	Benign	0.32
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs4712240; hg19: chr6-14752873;