4-39452170-A-G

Variant names:

• chr4-39452170-A-G
• rs10517522

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 0.286 in 151,902 control chromosomes in the GnomAD database, including 6,968 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 0.29 (6968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 19 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 (SAS) allele frequency at 95% confidence interval = 0.427 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: 0.286 AC: 43418 AN: 151786 Hom.: 6958 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.286 AC: 43439 AN: 151902 Hom.: 6968 Cov.: 31 AF XY: 0.293 AC XY: 21779 AN XY: 74226

African (AFR) AF: 0.136 AC: 5655 AN: 41450

American (AMR) AF: 0.366 AC: 5589 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2034 AN: 5156

South Asian (SAS) AF: 0.443 AC: 2129 AN: 4806

European-Finnish (FIN) AF: 0.371 AC: 3908 AN: 10524

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22302 AN: 67934

Other (OTH) AF: 0.272 AC: 574 AN: 2112

Alfa AF: 0.315 Hom.: 13590

Bravo AF: 0.276

Asia WGS AF: 0.433 AC: 1506 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	3.1
DANN	Benign	0.60
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs10517522; hg19: chr4-39453790;