chr6-14752642-C-T

Variant names:

• chr6-14752642-C-T
• rs4712240
• ENST00000629853.2:n.313+37348G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000629853.2(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 ENST00000629853.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000629853.2	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

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.885

Alfa AF: 0.896 Hom.: 26943

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4712240; hg19: chr6-14752873;