3-89952438-G-T

Variant names:

• chr3-89952438-G-T
• rs1521800

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 152,010 control chromosomes in the GnomAD database, including 10,236 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 (10236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.514 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: 49638 AN: 151894 Hom.: 10226 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.327 AC: 49655 AN: 152010 Hom.: 10236 Cov.: 32 AF XY: 0.328 AC XY: 24387 AN XY: 74292

African (AFR) AF: 0.0761 AC: 3161 AN: 41520

American (AMR) AF: 0.455 AC: 6938 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2434 AN: 5150

South Asian (SAS) AF: 0.531 AC: 2554 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3104 AN: 10550

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28583 AN: 67930

Other (OTH) AF: 0.365 AC: 771 AN: 2112

Alfa AF: 0.385 Hom.: 17294

Bravo AF: 0.325

Asia WGS AF: 0.457 AC: 1590 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	5.4
DANN	Benign	0.37
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1521800; hg19: chr3-90001588;