chr17-39884510-G-A

Variant names:

• chr17-39884510-G-A
• rs2872507

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 0.389 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
• Publications: 185 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.261 AC: 10801 AN: 41462

American (AMR) AF: 0.391 AC: 5971 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1397 AN: 5178

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4826

European-Finnish (FIN) AF: 0.532 AC: 5596 AN: 10528

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30683 AN: 67950

Other (OTH) AF: 0.374 AC: 788 AN: 2108

Alfa AF: 0.427 Hom.: 62476

Bravo AF: 0.367

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2872507; hg19: chr17-38040763;