6-156178397-C-T

Position:

• chr6-156178397-C-T

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.398+73923G>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 0.717 in 151,974 control chromosomes in the GnomAD database, including 39,746 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 0.72 (39746 hom., cov: 31)
• Consequence: ENST00000663591.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928923	XR_001744423.2	n.247-9903G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663591.1	n.398+73923G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108934 AN: 151858 Hom.: 39709 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.717 AC: 109019 AN: 151974 Hom.: 39746 Cov.: 31 AF XY: 0.719 AC XY: 53411 AN XY: 74284

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.688

Alfa AF: 0.699 Hom.: 16531

Bravo AF: 0.705

Asia WGS AF: 0.674 AC: 2342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.91
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9384428; hg19: chr6-156499531; COSMIC: COSV69431237;