3-187187998-T-C

Variant names:

• chr3-187187998-T-C
• rs9869355

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 0.323 in 152,086 control chromosomes in the GnomAD database, including 9,877 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 0.32 (9877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.323 AC: 49114 AN: 151968 Hom.: 9881 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.323 AC: 49096 AN: 152086 Hom.: 9877 Cov.: 32 AF XY: 0.323 AC XY: 23976 AN XY: 74328

African (AFR) AF: 0.0825 AC: 3426 AN: 41530

American (AMR) AF: 0.333 AC: 5091 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1392 AN: 3466

East Asian (EAS) AF: 0.180 AC: 933 AN: 5182

South Asian (SAS) AF: 0.363 AC: 1747 AN: 4808

European-Finnish (FIN) AF: 0.438 AC: 4620 AN: 10556

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30724 AN: 67952

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.401 Hom.: 6437

Bravo AF: 0.305

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs9869355; hg19: chr3-186905786;