6-126941943-A-G

Position:

• chr6-126941943-A-G

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.693+62242T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,974 control chromosomes in the GnomAD database, including 15,588 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 0.45 (15588 hom., cov: 32)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3716-22297T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651326.1	n.693+62242T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68500 AN: 151856 Hom.: 15582 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.451 AC: 68530 AN: 151974 Hom.: 15588 Cov.: 32 AF XY: 0.454 AC XY: 33751 AN XY: 74262

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.433

Alfa AF: 0.440 Hom.: 5215

Bravo AF: 0.450

Asia WGS AF: 0.492 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6907995; hg19: chr6-127263088;