rs1913081

Variant names:

• chr3-78393085-T-A
• rs1913081

Your query was ambiguous. Multiple possible variants found:

• chr3-78393085-T-A
• chr3-78393085-T-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 0.327 in 152,094 control chromosomes in the GnomAD database, including 8,642 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 0.33 (8642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.327 AC: 49762 AN: 151974 Hom.: 8637 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.327 AC: 49782 AN: 152094 Hom.: 8642 Cov.: 32 AF XY: 0.324 AC XY: 24103 AN XY: 74328

African (AFR) AF: 0.245 AC: 10182 AN: 41522

American (AMR) AF: 0.262 AC: 4002 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1199 AN: 5160

South Asian (SAS) AF: 0.279 AC: 1341 AN: 4812

European-Finnish (FIN) AF: 0.405 AC: 4284 AN: 10568

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25817 AN: 67980

Other (OTH) AF: 0.361 AC: 762 AN: 2110

Alfa AF: 0.334 Hom.: 1074

Bravo AF: 0.319

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.34
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1913081; hg19: chr3-78442235;