5-56756868-T-C

Variant names:

• chr5-56756868-T-C
• rs62355900

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 0.151 in 151,090 control chromosomes in the GnomAD database, including 2,122 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 (2122 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.151 AC: 22724 AN: 150968 Hom.: 2110 Cov.: 30

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.151 AC: 22759 AN: 151090 Hom.: 2122 Cov.: 30 AF XY: 0.155 AC XY: 11432 AN XY: 73698

African (AFR) AF: 0.0773 AC: 3190 AN: 41256

American (AMR) AF: 0.206 AC: 3104 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1765 AN: 5006

South Asian (SAS) AF: 0.320 AC: 1523 AN: 4752

European-Finnish (FIN) AF: 0.129 AC: 1343 AN: 10438

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10795 AN: 67788

Other (OTH) AF: 0.160 AC: 335 AN: 2098

Alfa AF: 0.158 Hom.: 5233

Bravo AF: 0.154

Asia WGS AF: 0.325 AC: 1127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs62355900; hg19: chr5-56052695;