chr5-56252970-T-C

Variant names:

• chr5-56252970-T-C
• rs32498

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 0.46 in 152,014 control chromosomes in the GnomAD database, including 19,452 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 0.46 (19452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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: 0.460 AC: 69803 AN: 151898 Hom.: 19413 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.460 AC: 69892 AN: 152014 Hom.: 19452 Cov.: 32 AF XY: 0.465 AC XY: 34537 AN XY: 74314

African (AFR) AF: 0.775 AC: 32166 AN: 41488

American (AMR) AF: 0.394 AC: 6021 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3467 AN: 5154

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4816

European-Finnish (FIN) AF: 0.371 AC: 3918 AN: 10552

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19665 AN: 67948

Other (OTH) AF: 0.429 AC: 903 AN: 2106

Alfa AF: 0.343 Hom.: 43364

Bravo AF: 0.472

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.65
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs32498; hg19: chr5-55548797; COSMIC: COSV60133736;