rs2872507

Positions:

• chr17-39884510-G-A
• chr17-39884510-G-T

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 0.389 in 152,006 control chromosomes in the GnomAD database, including 12,248 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 0.39 (12248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.389 AC: 59125 AN: 151888 Hom.: 12236 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.389 AC: 59173 AN: 152006 Hom.: 12248 Cov.: 32 AF XY: 0.392 AC XY: 29125 AN XY: 74300

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.374

Alfa AF: 0.433 Hom.: 31821

Bravo AF: 0.367

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2872507; hg19: chr17-38040763;