rs2317385

Variant names:

• chr17-47252316-G-A
• rs2317385

Your query was ambiguous. Multiple possible variants found:

• chr17-47252316-G-A
• chr17-47252316-G-C
• chr17-47252316-G-T

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 0.229 in 152,194 control chromosomes in the GnomAD database, including 4,791 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 0.23 (4791 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.629
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.229 AC: 34842 AN: 152076 Hom.: 4778 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.229 AC: 34897 AN: 152194 Hom.: 4791 Cov.: 33 AF XY: 0.231 AC XY: 17166 AN XY: 74404

African (AFR) AF: 0.348 AC: 14463 AN: 41506

American (AMR) AF: 0.151 AC: 2306 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2479 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1891 AN: 10600

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11268 AN: 68020

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.192 Hom.: 7531

Bravo AF: 0.235

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.30
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2317385; hg19: chr17-45329682;