rs3760468

Variant names:

• chr17-51153130-A-T
• rs3760468

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 0.386 in 151,962 control chromosomes in the GnomAD database, including 11,331 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 (11331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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: 0.386 AC: 58672 AN: 151842 Hom.: 11317 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.386 AC: 58724 AN: 151962 Hom.: 11331 Cov.: 32 AF XY: 0.383 AC XY: 28415 AN XY: 74278

African (AFR) AF: 0.375 AC: 15545 AN: 41428

American (AMR) AF: 0.406 AC: 6198 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1417 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5172

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4816

European-Finnish (FIN) AF: 0.363 AC: 3823 AN: 10544

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.396 AC: 26930 AN: 67968

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.397 Hom.: 1531

Bravo AF: 0.391

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		0.023
PromoterAI		-0.00060	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760468; hg19: chr17-49230491;