rs17166803

chr7-13150255-C-T

Variant summary

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

The ENST00000639998.1(ENSG00000229618):n.484-67290C>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 0.0183 in 152,162 control chromosomes in the GnomAD database, including 92 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 0.018 (92 hom., cov: 32)
• Consequence: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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
	ENST00000639998.1	n.484-67290C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2793 AN: 152044 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00336

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0183 AC: 2786 AN: 152162 Hom.: 92 Cov.: 32 AF XY: 0.0196 AC XY: 1461 AN XY: 74396

Gnomad4 AFR AF: 0.00335

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0141 Hom.: 6

Bravo AF: 0.0189

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17166803; hg19: chr7-13189880;