rs11949391

chr5-56749254-T-Cchr5-56749254-T-G

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 0.138 in 152,026 control chromosomes in the GnomAD database, including 1,642 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 0.14 (1642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542

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 (SAS) allele frequency at 95% confidence interval = 0.164 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: 0.138 AC: 21036 AN: 151908 Hom.: 1642 Cov.: 31

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.138 AC: 21041 AN: 152026 Hom.: 1642 Cov.: 31 AF XY: 0.140 AC XY: 10414 AN XY: 74326

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.134

Alfa AF: 0.121 Hom.: 372

Bravo AF: 0.135

Asia WGS AF: 0.0920 AC: 320 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	5.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11949391; hg19: chr5-56045081;