6-126665850-A-G

Variant names:

• chr6-126665850-A-G
• rs1262476
• ENST00000650727.1:n.1167-43977T>C

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.1167-43977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 151,980 control chromosomes in the GnomAD database, including 50,598 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 0.81 (50598 hom., cov: 31)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 19 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377992	XR_001743836.2	n.912+4564A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650727.1	n.1167-43977T>C		intron_variant	Intron 9 of 14
ENSG00000293110	ENST00000651326.1	n.694-62385T>C		intron_variant	Intron 3 of 6
ENSG00000293110	ENST00000652545.1	n.1477-43977T>C		intron_variant	Intron 10 of 15

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123445 AN: 151862 Hom.: 50549 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.813 AC: 123547 AN: 151980 Hom.: 50598 Cov.: 31 AF XY: 0.817 AC XY: 60691 AN XY: 74258

African (AFR) AF: 0.892 AC: 37012 AN: 41488

American (AMR) AF: 0.847 AC: 12910 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2843 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5039 AN: 5148

South Asian (SAS) AF: 0.766 AC: 3692 AN: 4822

European-Finnish (FIN) AF: 0.807 AC: 8520 AN: 10558

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.749 AC: 50884 AN: 67944

Other (OTH) AF: 0.815 AC: 1722 AN: 2112

Alfa AF: 0.779 Hom.: 67743

Bravo AF: 0.824

Asia WGS AF: 0.827 AC: 2873 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.38
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1262476; hg19: chr6-126986996; COSMIC: COSV60280568;