rs3729535

Variant names:

• chr19-2475687-C-A
• rs3729535

Your query was ambiguous. Multiple possible variants found:

• chr19-2475687-C-A
• chr19-2475687-C-G

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 0.0863 in 152,122 control chromosomes in the GnomAD database, including 613 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 0.086 (613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0941 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: 0.0861 AC: 13087 AN: 152004 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0810

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0863 AC: 13130 AN: 152122 Hom.: 613 Cov.: 32 AF XY: 0.0845 AC XY: 6286 AN XY: 74382

African (AFR) AF: 0.0966 AC: 4008 AN: 41500

American (AMR) AF: 0.0809 AC: 1234 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3470

East Asian (EAS) AF: 0.0531 AC: 274 AN: 5156

South Asian (SAS) AF: 0.0753 AC: 363 AN: 4822

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10610

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6195 AN: 67990

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0808 Hom.: 378

Bravo AF: 0.0910

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.70
PhyloP100		0.011
PromoterAI		-0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3729535; hg19: chr19-2475685;