rs2470209

Variant names:

• chr17-32912311-G-A
• rs2470209

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 0.442 in 152,018 control chromosomes in the GnomAD database, including 15,646 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 0.44 (15646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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 (AFR) allele frequency at 95% confidence interval = 0.575 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: 0.442 AC: 67082 AN: 151898 Hom.: 15625 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.442 AC: 67150 AN: 152018 Hom.: 15646 Cov.: 32 AF XY: 0.436 AC XY: 32407 AN XY: 74298

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.437

Alfa AF: 0.412 Hom.: 2857

Bravo AF: 0.467

Asia WGS AF: 0.422 AC: 1473 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	12
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2470209; hg19: chr17-31239329;