chr14-68871717-C-T

Variant names:

• chr14-68871717-C-T
• rs4312253

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 0.69 in 152,028 control chromosomes in the GnomAD database, including 36,371 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 0.69 (36371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 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: 0.690 AC: 104849 AN: 151910 Hom.: 36341 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.690 AC: 104923 AN: 152028 Hom.: 36371 Cov.: 31 AF XY: 0.691 AC XY: 51345 AN XY: 74326

African (AFR) AF: 0.676 AC: 28019 AN: 41442

American (AMR) AF: 0.768 AC: 11738 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2514 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2596 AN: 5162

South Asian (SAS) AF: 0.751 AC: 3609 AN: 4808

European-Finnish (FIN) AF: 0.666 AC: 7040 AN: 10572

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47105 AN: 67984

Other (OTH) AF: 0.694 AC: 1462 AN: 2106

Alfa AF: 0.684 Hom.: 4628

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4312253; hg19: chr14-69338434;