chr14-42855003-A-C

Variant names:

• chr14-42855003-A-C
• rs2044747

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 0.604 in 152,016 control chromosomes in the GnomAD database, including 30,314 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 0.60 (30314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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: 0.604 AC: 91745 AN: 151898 Hom.: 30306 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.604 AC: 91788 AN: 152016 Hom.: 30314 Cov.: 32 AF XY: 0.612 AC XY: 45517 AN XY: 74326

African (AFR) AF: 0.318 AC: 13168 AN: 41460

American (AMR) AF: 0.643 AC: 9807 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4240 AN: 5158

South Asian (SAS) AF: 0.703 AC: 3395 AN: 4828

European-Finnish (FIN) AF: 0.799 AC: 8444 AN: 10574

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48063 AN: 67960

Other (OTH) AF: 0.645 AC: 1364 AN: 2116

Alfa AF: 0.678 Hom.: 51709

Bravo AF: 0.582

Asia WGS AF: 0.746 AC: 2587 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.42
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs2044747; hg19: chr14-43324206;