rs657223

Variant names:

• chr5-135020110-A-T
• rs657223

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 0.385 in 151,922 control chromosomes in the GnomAD database, including 12,097 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 0.39 (12097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.549 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: 0.385 AC: 58450 AN: 151804 Hom.: 12072 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.385 AC: 58502 AN: 151922 Hom.: 12097 Cov.: 32 AF XY: 0.389 AC XY: 28854 AN XY: 74270

African (AFR) AF: 0.246 AC: 10175 AN: 41440

American (AMR) AF: 0.496 AC: 7578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2835 AN: 5148

South Asian (SAS) AF: 0.567 AC: 2722 AN: 4800

European-Finnish (FIN) AF: 0.382 AC: 4031 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28595 AN: 67908

Other (OTH) AF: 0.385 AC: 811 AN: 2104

Alfa AF: 0.397 Hom.: 1550

Bravo AF: 0.383

Asia WGS AF: 0.577 AC: 2006 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	0.70
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs657223; hg19: chr5-134355800; COSMIC: COSV60199571;