rs1081681

Positions:

• chr17-35328755-T-G

Variant summary

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

The variant allele was found at a frequency of 0.622 in 152,042 control chromosomes in the GnomAD database, including 31,617 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 0.62 (31617 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.35328755T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94492 AN: 151924 Hom.: 31566 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.622 AC: 94603 AN: 152042 Hom.: 31617 Cov.: 32 AF XY: 0.617 AC XY: 45862 AN XY: 74306

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.586

Alfa AF: 0.590 Hom.: 3468

Bravo AF: 0.644

Asia WGS AF: 0.535 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1081681; hg19: chr17-33655774; COSMIC: COSV73952688;