6-127114919-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000651326.1(ENSG00000293110):n.404+4418G>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 0.512 in 152,074 control chromosomes in the GnomAD database, including 19,937 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 0.51 (19937 hom., cov: 33)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377989	XR_002956387.2	n.3325+3982G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651326.1	n.404+4418G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77826 AN: 151954 Hom.: 19920 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.512 AC: 77892 AN: 152074 Hom.: 19937 Cov.: 33 AF XY: 0.508 AC XY: 37756 AN XY: 74328

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.485

Alfa AF: 0.517 Hom.: 16617

Bravo AF: 0.514

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	16
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936800; hg19: chr6-127436064; COSMIC: COSV63150114;