rs941838

chr14-99950319-C-Achr14-99950319-C-Gchr14-99950319-C-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 0.9 in 152,182 control chromosomes in the GnomAD database, including 62,280 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 0.90 (62280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.900 AC: 136863 AN: 152064 Hom.: 62243 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.900 AC: 136953 AN: 152182 Hom.: 62280 Cov.: 31 AF XY: 0.904 AC XY: 67241 AN XY: 74396

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.929

Alfa AF: 0.918 Hom.: 9412

Bravo AF: 0.892

Asia WGS AF: 0.950 AC: 3305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941838; hg19: chr14-100416656;