rs1499646

chr8-74155877-C-T

Variant summary

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

The ENST00000668834.1(ENSG00000253983):n.176-10148C>T 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 0.761 in 151,956 control chromosomes in the GnomAD database, including 44,777 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 0.76 (44777 hom., cov: 30)
• Consequence: ENST00000668834.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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
	ENST00000668834.1	n.176-10148C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115638 AN: 151838 Hom.: 44765 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.837

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.761 AC: 115700 AN: 151956 Hom.: 44777 Cov.: 30 AF XY: 0.762 AC XY: 56627 AN XY: 74282

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.791

Alfa AF: 0.794 Hom.: 24016

Bravo AF: 0.758

Asia WGS AF: 0.806 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	14
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499646; hg19: chr8-75068112;