rs4904947

chr14-92505818-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 0.203 in 152,132 control chromosomes in the GnomAD database, including 3,829 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 0.20 (3829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 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: 0.203 AC: 30901 AN: 152014 Hom.: 3832 Cov.: 32

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.203 AC: 30908 AN: 152132 Hom.: 3829 Cov.: 32 AF XY: 0.209 AC XY: 15540 AN XY: 74342

Gnomad4 AFR AF: 0.0649

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.225

Alfa AF: 0.242 Hom.: 8634

Bravo AF: 0.199

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4904947; hg19: chr14-92972162;