rs7015657

Positions:

• chr8-21110040-C-G

Variant summary

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

The ENST00000659453.1(ENSG00000254092):​n.1640-50105G>C 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 0.301 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: ENST00000659453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659453.1	n.1640-50105G>C		intron_variant, non_coding_transcript_variant

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;