rs1947339

Positions:

• chr5-4966904-C-A
• chr5-4966904-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 0.372 in 151,894 control chromosomes in the GnomAD database, including 10,726 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 0.37 (10726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.372 AC: 56413 AN: 151776 Hom.: 10714 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.372 AC: 56471 AN: 151894 Hom.: 10726 Cov.: 32 AF XY: 0.373 AC XY: 27662 AN XY: 74208

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.339

Alfa AF: 0.268 Hom.: 839

Bravo AF: 0.372

Asia WGS AF: 0.400 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.048
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1947339; hg19: chr5-4967017;