6-88185415-G-T

Variant names:

• chr6-88185415-G-T
• rs1884831
• ENST00000756466.1:n.157C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000756466.1(ENSG00000234426):​n.157C>A variant causes a non coding transcript exon 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: ENSG00000234426 ENST00000756466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 2 publications found

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234426	ENST00000756466.1	n.157C>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000234426	ENST00000756467.1	n.140C>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000234426	ENST00000756468.1	n.180C>A		non_coding_transcript_exon_variant	Exon 1 of 2

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

African (AFR) AF: 0.371 AC: 15368 AN: 41438

American (AMR) AF: 0.568 AC: 8679 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.800 AC: 4132 AN: 5162

South Asian (SAS) AF: 0.571 AC: 2751 AN: 4818

European-Finnish (FIN) AF: 0.543 AC: 5710 AN: 10520

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36505 AN: 67960

Other (OTH) AF: 0.499 AC: 1053 AN: 2110

Alfa AF: 0.536 Hom.: 7403

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1884831; hg19: chr6-88895134;