rs17488409

Variant names:

• chr12-18747035-A-G
• rs17488409

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0520 AC: 2162 AN: 41562

American (AMR) AF: 0.0479 AC: 732 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 376 AN: 3464

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4824

European-Finnish (FIN) AF: 0.0414 AC: 440 AN: 10618

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4061 AN: 68014

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0585 Hom.: 280

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17488409; hg19: chr12-18899969;