14-68866421-C-G

Variant names:

• chr14-68866421-C-G
• rs1742890

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 151,740 control chromosomes in the GnomAD database, including 36,343 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 (36343 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.761 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: 104681 AN: 151622 Hom.: 36315 Cov.: 29

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.690 AC: 104753 AN: 151740 Hom.: 36343 Cov.: 29 AF XY: 0.691 AC XY: 51238 AN XY: 74138

African (AFR) AF: 0.675 AC: 27929 AN: 41372

American (AMR) AF: 0.773 AC: 11770 AN: 15232

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

East Asian (EAS) AF: 0.501 AC: 2570 AN: 5130

South Asian (SAS) AF: 0.749 AC: 3600 AN: 4806

European-Finnish (FIN) AF: 0.666 AC: 7013 AN: 10536

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

European-Non Finnish (NFE) AF: 0.693 AC: 47056 AN: 67894

Other (OTH) AF: 0.694 AC: 1458 AN: 2100

Alfa AF: 0.590 Hom.: 1612

Bravo AF: 0.696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.55
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1742890; hg19: chr14-69333138;