rs17741410

Variant names:

• chr8-85319836-A-G
• rs17741410

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;