rs6459375

Variant names:

• chr6-14741075-G-T
• rs6459375
• ENST00000629853.3:n.313+48915C>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+48915C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,158 control chromosomes in the GnomAD database, including 56,156 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 0.85 (56156 hom., cov: 31)
• Consequence: ENSG00000234261 ENST00000629853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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+48915C>A		intron_variant	Intron 3 of 3	5
ENSG00000234261	ENST00000689305.1	n.179-24C>A		intron_variant	Intron 1 of 2
ENSG00000234261	ENST00000702363.1	n.187-9597C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129980 AN: 152040 Hom.: 56127 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.855 AC: 130060 AN: 152158 Hom.: 56156 Cov.: 31 AF XY: 0.857 AC XY: 63779 AN XY: 74414

African (AFR) AF: 0.725 AC: 30057 AN: 41466

American (AMR) AF: 0.864 AC: 13213 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3260 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5032 AN: 5186

South Asian (SAS) AF: 0.910 AC: 4393 AN: 4830

European-Finnish (FIN) AF: 0.911 AC: 9655 AN: 10596

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61579 AN: 67992

Other (OTH) AF: 0.863 AC: 1827 AN: 2116

Alfa AF: 0.891 Hom.: 30098

Bravo AF: 0.843

Asia WGS AF: 0.913 AC: 3176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs6459375; hg19: chr6-14741306;