6-126514509-C-T

Variant names:

• chr6-126514509-C-T
• rs1490388
• ENST00000650727.1:n.3037-16984G>A

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.3037-16984G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,972 control chromosomes in the GnomAD database, including 16,447 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 (16447 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 43 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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
ENSG00000293110	ENST00000650727.1	n.3037-16984G>A		intron_variant	Intron 14 of 14
ENSG00000293110	ENST00000651326.1	n.2290-41915G>A		intron_variant	Intron 5 of 6
ENSG00000293110	ENST00000652383.1	n.630+17154G>A		intron_variant	Intron 3 of 4
ENSG00000293110	ENST00000652545.1	n.3347-16984G>A		intron_variant	Intron 15 of 15

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65547 AN: 151852 Hom.: 16445 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.431 AC: 65553 AN: 151972 Hom.: 16447 Cov.: 32 AF XY: 0.442 AC XY: 32792 AN XY: 74264

African (AFR) AF: 0.210 AC: 8721 AN: 41478

American (AMR) AF: 0.609 AC: 9299 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1678 AN: 3462

East Asian (EAS) AF: 0.974 AC: 5038 AN: 5172

South Asian (SAS) AF: 0.675 AC: 3258 AN: 4824

European-Finnish (FIN) AF: 0.437 AC: 4617 AN: 10560

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31339 AN: 67910

Other (OTH) AF: 0.465 AC: 980 AN: 2108

Alfa AF: 0.465 Hom.: 41349

Bravo AF: 0.437

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1490388; hg19: chr6-126835655; COSMIC: COSV60280248;