rs17741410

Positions:

• chr8-85319836-A-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 0.129 in 152,194 control chromosomes in the GnomAD database, including 1,527 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 0.13 (1527 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85319836A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19585 AN: 152076 Hom.: 1526 Cov.: 31

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.129 AC: 19595 AN: 152194 Hom.: 1527 Cov.: 31 AF XY: 0.128 AC XY: 9503 AN XY: 74402

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.0878

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.118

Alfa AF: 0.166 Hom.: 2496

Bravo AF: 0.116

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17741410; hg19: chr8-86232065;