rs2872507

Variant names:

• chr17-39884510-G-A
• rs2872507

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;