rs11949278

chr5-163625311-T-C

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 0.208 in 152,126 control chromosomes in the GnomAD database, including 4,084 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 0.21 (4084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.208 AC: 31642 AN: 152008 Hom.: 4081 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.208 AC: 31682 AN: 152126 Hom.: 4084 Cov.: 32 AF XY: 0.204 AC XY: 15149 AN XY: 74384

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.210

Alfa AF: 0.188 Hom.: 738

Bravo AF: 0.218

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	11
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11949278; hg19: chr5-163052317;