rs714421

Variant names:

• chr14-70892868-T-C
• rs714421

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 0.473 in 152,002 control chromosomes in the GnomAD database, including 18,414 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 0.47 (18414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.581 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: 0.473 AC: 71902 AN: 151884 Hom.: 18408 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.473 AC: 71933 AN: 152002 Hom.: 18414 Cov.: 32 AF XY: 0.472 AC XY: 35081 AN XY: 74296

African (AFR) AF: 0.306 AC: 12669 AN: 41436

American (AMR) AF: 0.387 AC: 5911 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1421 AN: 5178

South Asian (SAS) AF: 0.550 AC: 2644 AN: 4810

European-Finnish (FIN) AF: 0.587 AC: 6196 AN: 10552

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39791 AN: 67956

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.542 Hom.: 102193

Bravo AF: 0.448

Asia WGS AF: 0.461 AC: 1601 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	6.1
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs714421; hg19: chr14-71359585;