6-88185415-G-T

Position:

• chr6-88185415-G-T

Variant summary

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

The ENST00000648572.1(ENSG00000234426):​n.991-6981C>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 0.504 in 151,950 control chromosomes in the GnomAD database, including 20,085 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 0.50 (20085 hom., cov: 32)
• Consequence: ENST00000648572.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 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
	ENST00000648572.1	n.991-6981C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76567 AN: 151832 Hom.: 20073 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.504 AC: 76610 AN: 151950 Hom.: 20085 Cov.: 32 AF XY: 0.509 AC XY: 37802 AN XY: 74238

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.499

Alfa AF: 0.526 Hom.: 3533

Bravo AF: 0.500

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
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: rs1884831; hg19: chr6-88895134;