rs17430337

chr6-102523371-G-A

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 0.0388 in 151,972 control chromosomes in the GnomAD database, including 149 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 0.039 (149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.052 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

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5888 AN: 151854 Hom.: 149 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0388 AC: 5894 AN: 151972 Hom.: 149 Cov.: 32 AF XY: 0.0367 AC XY: 2724 AN XY: 74272

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0405 Hom.: 172

Bravo AF: 0.0406

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.73
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17430337; hg19: chr6-102971246;