rs2044747

chr14-42855003-A-Cchr14-42855003-A-Gchr14-42855003-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.645

Alfa AF: 0.684 Hom.: 45647

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2044747; hg19: chr14-43324206;