chr5-56757652-C-T

Variant names:

• chr5-56757652-C-T
• rs74345699

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 0.148 in 152,202 control chromosomes in the GnomAD database, including 2,133 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 0.15 (2133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22539 AN: 152084 Hom.: 2122 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.148 AC: 22570 AN: 152202 Hom.: 2133 Cov.: 32 AF XY: 0.154 AC XY: 11446 AN XY: 74404

African (AFR) AF: 0.0637 AC: 2648 AN: 41558

American (AMR) AF: 0.208 AC: 3176 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1873 AN: 5166

South Asian (SAS) AF: 0.324 AC: 1564 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10592

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10848 AN: 67986

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.0764 Hom.: 98

Bravo AF: 0.149

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.96
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs74345699; hg19: chr5-56053479;