rs2470209

Positions:

• chr17-32912311-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 0.442 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;