chr5-56749254-T-C

Variant names:

• chr5-56749254-T-C
• rs11949391

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0943 AC: 3914 AN: 41494

American (AMR) AF: 0.166 AC: 2526 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.0434 AC: 225 AN: 5182

South Asian (SAS) AF: 0.174 AC: 838 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10942 AN: 67928

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.149 Hom.: 3204

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs11949391; hg19: chr5-56045081;