rs1538956

Positions:

• chr6-126642880-G-T

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.694-39415C>A 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 151,984 control chromosomes in the GnomAD database, including 18,000 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 (18000 hom., cov: 32)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651326.1	n.694-39415C>A		intron_variant, non_coding_transcript_variant
	ENST00000650727.1	n.1167-21007C>A		intron_variant, non_coding_transcript_variant
	ENST00000652545.1	n.1477-21007C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68555 AN: 151866 Hom.: 17996 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.451 AC: 68560 AN: 151984 Hom.: 18000 Cov.: 32 AF XY: 0.462 AC XY: 34311 AN XY: 74296

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.480

Alfa AF: 0.487 Hom.: 9374

Bravo AF: 0.455

Asia WGS AF: 0.703 AC: 2440 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	0.78
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538956; hg19: chr6-126964026; COSMIC: COSV69095951;