rs11949278

Variant names:

• chr5-163625311-T-C
• rs11949278

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;