rs1039991

Variant names:

• chr3-89509161-C-G
• rs1039991

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 0.253 in 149,706 control chromosomes in the GnomAD database, including 5,094 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 0.25 (5094 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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: 0.253 AC: 37884 AN: 149568 Hom.: 5093 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0744

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.253 AC: 37908 AN: 149706 Hom.: 5094 Cov.: 31 AF XY: 0.254 AC XY: 18542 AN XY: 73128

African (AFR) AF: 0.251 AC: 10300 AN: 41032

American (AMR) AF: 0.218 AC: 3274 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 528 AN: 3452

East Asian (EAS) AF: 0.0935 AC: 441 AN: 4716

South Asian (SAS) AF: 0.102 AC: 447 AN: 4372

European-Finnish (FIN) AF: 0.409 AC: 4220 AN: 10322

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18142 AN: 67478

Other (OTH) AF: 0.215 AC: 451 AN: 2100

Alfa AF: 0.263 Hom.: 673

Bravo AF: 0.237

Asia WGS AF: 0.0970 AC: 335 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1039991; hg19: chr3-89558311;