chr8-21110040-C-G

Variant names:

• chr8-21110040-C-G
• rs7015657
• ENST00000657283.1:n.2001+688G>C

Variant summary

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

The ENST00000657283.1(ENSG00000254092):​n.2001+688G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,012 control chromosomes in the GnomAD database, including 7,126 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 0.30 (7126 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657283.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 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
ENSG00000254092	ENST00000657283.1	n.2001+688G>C		intron_variant	Intron 1 of 3
ENSG00000254092	ENST00000657734.1	n.1327-50105G>C		intron_variant	Intron 2 of 4
ENSG00000254092	ENST00000659453.1	n.1640-50105G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45674 AN: 151892 Hom.: 7119 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.301 AC: 45713 AN: 152012 Hom.: 7126 Cov.: 32 AF XY: 0.305 AC XY: 22653 AN XY: 74282

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.311

Alfa AF: 0.291 Hom.: 807

Bravo AF: 0.299

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7015657; hg19: chr8-20967551;