rs944398

Variant names:

• chr14-20064220-T-C
• rs944398

Your query was ambiguous. Multiple possible variants found:

• chr14-20064220-T-C
• chr14-20064220-T-G

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 0.439 in 148,236 control chromosomes in the GnomAD database, including 14,566 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 0.44 (14566 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 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: 0.438 AC: 64948 AN: 148146 Hom.: 14531 Cov.: 25

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.439 AC: 65033 AN: 148236 Hom.: 14566 Cov.: 25 AF XY: 0.442 AC XY: 31878 AN XY: 72048

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.433

Alfa AF: 0.400 Hom.: 1964

Bravo AF: 0.446

Asia WGS AF: 0.612 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs944398; hg19: chr14-20532379;