5-57062320-G-C

Variant names:

• chr5-57062320-G-C
• rs831818

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 0.545 in 152,100 control chromosomes in the GnomAD database, including 22,962 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 0.54 (22962 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 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: 0.545 AC: 82760 AN: 151980 Hom.: 22943 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.545 AC: 82841 AN: 152100 Hom.: 22962 Cov.: 33 AF XY: 0.541 AC XY: 40204 AN XY: 74342

African (AFR) AF: 0.544 AC: 22550 AN: 41480

American (AMR) AF: 0.549 AC: 8394 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5178

South Asian (SAS) AF: 0.499 AC: 2401 AN: 4812

European-Finnish (FIN) AF: 0.537 AC: 5671 AN: 10560

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38855 AN: 67994

Other (OTH) AF: 0.547 AC: 1156 AN: 2114

Alfa AF: 0.560 Hom.: 2966

Bravo AF: 0.539

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.7
DANN	Benign	0.42
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs831818; hg19: chr5-56358147;