rs876287

Variant names:

• chr14-82954380-T-C
• rs876287

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 0.332 in 151,852 control chromosomes in the GnomAD database, including 8,522 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 (8522 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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: 0.332 AC: 50372 AN: 151734 Hom.: 8522 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.332 AC: 50392 AN: 151852 Hom.: 8522 Cov.: 31 AF XY: 0.332 AC XY: 24618 AN XY: 74190

African (AFR) AF: 0.351 AC: 14542 AN: 41378

American (AMR) AF: 0.245 AC: 3737 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1544 AN: 5130

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4812

European-Finnish (FIN) AF: 0.367 AC: 3869 AN: 10550

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22747 AN: 67944

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.334 Hom.: 5835

Bravo AF: 0.325

Asia WGS AF: 0.321 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.47
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs876287; hg19: chr14-83420724;