rs3899033

Variant names:

• chr5-175787072-G-A
• rs3899033

Your query was ambiguous. Multiple possible variants found:

• chr5-175787072-G-A
• chr5-175787072-G-T

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 0.138 in 152,174 control chromosomes in the GnomAD database, including 1,969 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 0.14 (1969 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.138 AC: 20972 AN: 152056 Hom.: 1965 Cov.: 34

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.138 AC: 20992 AN: 152174 Hom.: 1969 Cov.: 34 AF XY: 0.135 AC XY: 10073 AN XY: 74392

African (AFR) AF: 0.257 AC: 10664 AN: 41490

American (AMR) AF: 0.0888 AC: 1357 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3470

East Asian (EAS) AF: 0.0953 AC: 494 AN: 5184

South Asian (SAS) AF: 0.199 AC: 961 AN: 4820

European-Finnish (FIN) AF: 0.0742 AC: 787 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5940 AN: 68006

Other (OTH) AF: 0.117 AC: 247 AN: 2112

Alfa AF: 0.112 Hom.: 1490

Bravo AF: 0.143

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.4
DANN	Benign	0.76
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3899033; hg19: chr5-175214075;