6-88185158-C-G

Variant names:

• chr6-88185158-C-G
• rs1884830
• ENST00000756467.1:n.397G>C

Variant summary

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

The ENST00000756467.1(ENSG00000234426):​n.397G>C 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 0.0834 in 152,166 control chromosomes in the GnomAD database, including 636 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 0.083 (636 hom., cov: 32)
• Consequence: ENSG00000234426 ENST00000756467.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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	ENST00000756467.1	n.397G>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000234426	ENST00000756468.1	n.437G>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000234426	ENST00000648572.1	n.991-6724G>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12697 AN: 152048 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0834 AC: 12698 AN: 152166 Hom.: 636 Cov.: 32 AF XY: 0.0821 AC XY: 6111 AN XY: 74400

African (AFR) AF: 0.0333 AC: 1381 AN: 41502

American (AMR) AF: 0.0585 AC: 894 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3466

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5164

South Asian (SAS) AF: 0.143 AC: 688 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1118 AN: 10588

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7967 AN: 68020

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0390 Hom.: 40

Bravo AF: 0.0770

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.60
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1884830; hg19: chr6-88894877;