rs17488409

chr12-18747035-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 0.0532 in 152,268 control chromosomes in the GnomAD database, including 245 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 0.053 (245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0582 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: 0.0532 AC: 8100 AN: 152150 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0532 AC: 8102 AN: 152268 Hom.: 245 Cov.: 32 AF XY: 0.0511 AC XY: 3802 AN XY: 74440

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0590 Hom.: 215

Bravo AF: 0.0550

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17488409; hg19: chr12-18899969;