rs17642091

Positions:

• chr17-78332756-G-A
• chr17-78332756-G-T

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-11209G>A 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 0.136 in 152,122 control chromosomes in the GnomAD database, including 2,015 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 0.14 (2015 hom., cov: 31)
• Consequence: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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 (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586321.1	n.61-11209G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20718 AN: 152004 Hom.: 2017 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.136 AC: 20720 AN: 152122 Hom.: 2015 Cov.: 31 AF XY: 0.138 AC XY: 10226 AN XY: 74326

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.119

Alfa AF: 0.170 Hom.: 1716

Bravo AF: 0.117

Asia WGS AF: 0.0370 AC: 127 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	3.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17642091; hg19: chr17-76328837;