rs3850301

Variant names:

• chr14-58614414-T-C
• rs3850301

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 0.272 in 152,184 control chromosomes in the GnomAD database, including 6,060 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 0.27 (6060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• 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 (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.272 AC: 41311 AN: 152066 Hom.: 6044 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.272 AC: 41370 AN: 152184 Hom.: 6060 Cov.: 33 AF XY: 0.265 AC XY: 19736 AN XY: 74406

African (AFR) AF: 0.355 AC: 14736 AN: 41502

American (AMR) AF: 0.223 AC: 3408 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5188

South Asian (SAS) AF: 0.126 AC: 607 AN: 4828

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18608 AN: 67996

Other (OTH) AF: 0.278 AC: 588 AN: 2116

Alfa AF: 0.255 Hom.: 925

Bravo AF: 0.277

Asia WGS AF: 0.101 AC: 353 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	6.3
DANN	Benign	0.51
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3850301; hg19: chr14-59081132;