chr5-56757896-A-T

Variant names:

• chr5-56757896-A-T
• rs62355902

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 0.158 in 152,102 control chromosomes in the GnomAD database, including 2,302 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 0.16 (2302 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.158 AC: 23974 AN: 151984 Hom.: 2286 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.158 AC: 24012 AN: 152102 Hom.: 2302 Cov.: 32 AF XY: 0.163 AC XY: 12150 AN XY: 74368

African (AFR) AF: 0.0913 AC: 3793 AN: 41522

American (AMR) AF: 0.214 AC: 3262 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3468

East Asian (EAS) AF: 0.388 AC: 2000 AN: 5152

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10598

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10900 AN: 67966

Other (OTH) AF: 0.168 AC: 353 AN: 2106

Alfa AF: 0.159 Hom.: 242

Bravo AF: 0.160

Asia WGS AF: 0.341 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.28
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs62355902; hg19: chr5-56053723;