6-89141287-A-C

Position:

• chr6-89141287-A-C

Variant summary

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

The ENST00000657573.1(ENSG00000288009):​n.380+2460T>G 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 0.362 in 152,068 control chromosomes in the GnomAD database, including 10,943 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 0.36 (10943 hom., cov: 32)
• Consequence: ENST00000657573.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929004	XR_942766.4	n.1261+2460T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657573.1	n.380+2460T>G		intron_variant, non_coding_transcript_variant
	ENST00000664569.1	n.333+2460T>G		intron_variant, non_coding_transcript_variant
	ENST00000665193.1	n.431+2379T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54923 AN: 151950 Hom.: 10890 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.362 AC: 55041 AN: 152068 Hom.: 10943 Cov.: 32 AF XY: 0.356 AC XY: 26452 AN XY: 74332

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.367

Alfa AF: 0.338 Hom.: 1604

Bravo AF: 0.381

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4707518; hg19: chr6-89851006;