8-85836942-G-T

Variant names:

• chr8-85836942-G-T
• rs2930553
• ENST00000648211.1:n.399+3167G>T

Variant summary

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

The ENST00000648211.1(ENSG00000253154):​n.399+3167G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,986 control chromosomes in the GnomAD database, including 13,924 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 0.40 (13924 hom., cov: 32)
• Consequence: ENSG00000253154 ENST00000648211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 5 publications found

Genes affected

ENSG00000253154 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 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
ENSG00000253154	ENST00000648211.1	n.399+3167G>T		intron_variant	Intron 1 of 2
ENSG00000253154	ENST00000757295.1	n.235+10450G>T		intron_variant	Intron 1 of 3
ENSG00000253154	ENST00000757296.1	n.404+3167G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60926 AN: 151868 Hom.: 13919 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.401 AC: 60947 AN: 151986 Hom.: 13924 Cov.: 32 AF XY: 0.401 AC XY: 29754 AN XY: 74274

African (AFR) AF: 0.173 AC: 7154 AN: 41468

American (AMR) AF: 0.422 AC: 6446 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1708 AN: 3470

East Asian (EAS) AF: 0.596 AC: 3060 AN: 5130

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4822

European-Finnish (FIN) AF: 0.539 AC: 5690 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34109 AN: 67962

Other (OTH) AF: 0.389 AC: 819 AN: 2108

Alfa AF: 0.451 Hom.: 8170

Bravo AF: 0.388

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.70
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2930553; hg19: chr8-86849171;