rs1915304

Variant names:

• chr3-89655243-C-T
• rs1915304

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 0.222 in 150,138 control chromosomes in the GnomAD database, including 4,051 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 0.22 (4051 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 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: 0.222 AC: 33254 AN: 150028 Hom.: 4051 Cov.: 24

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.222 AC: 33270 AN: 150138 Hom.: 4051 Cov.: 24 AF XY: 0.223 AC XY: 16316 AN XY: 73208

African (AFR) AF: 0.171 AC: 7009 AN: 40912

American (AMR) AF: 0.196 AC: 2931 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3456

East Asian (EAS) AF: 0.123 AC: 618 AN: 5034

South Asian (SAS) AF: 0.0913 AC: 434 AN: 4754

European-Finnish (FIN) AF: 0.399 AC: 4061 AN: 10170

Middle Eastern (MID) AF: 0.0966 AC: 28 AN: 290

European-Non Finnish (NFE) AF: 0.257 AC: 17351 AN: 67544

Other (OTH) AF: 0.186 AC: 387 AN: 2086

Alfa AF: 0.232 Hom.: 3229

Bravo AF: 0.205

Asia WGS AF: 0.114 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.58
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1915304; hg19: chr3-89704393;