rs295301

Variant names:

• chr3-141619799-G-A
• rs295301

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 0.38 in 151,992 control chromosomes in the GnomAD database, including 11,108 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 0.38 (11108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.380 AC: 57645 AN: 151872 Hom.: 11094 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.380 AC: 57687 AN: 151992 Hom.: 11108 Cov.: 32 AF XY: 0.381 AC XY: 28275 AN XY: 74308

African (AFR) AF: 0.436 AC: 18065 AN: 41438

American (AMR) AF: 0.422 AC: 6448 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1895 AN: 5164

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4820

European-Finnish (FIN) AF: 0.346 AC: 3651 AN: 10548

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23491 AN: 67958

Other (OTH) AF: 0.372 AC: 785 AN: 2108

Alfa AF: 0.354 Hom.: 20608

Bravo AF: 0.386

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs295301; hg19: chr3-141338641;