5-56293348-C-T

Variant names:

• chr5-56293348-C-T
• rs7379332

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 0.259 in 152,068 control chromosomes in the GnomAD database, including 6,157 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 0.26 (6157 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.259 AC: 39401 AN: 151950 Hom.: 6154 Cov.: 31

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.259 AC: 39412 AN: 152068 Hom.: 6157 Cov.: 31 AF XY: 0.263 AC XY: 19580 AN XY: 74342

African (AFR) AF: 0.0918 AC: 3811 AN: 41504

American (AMR) AF: 0.288 AC: 4398 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3464

East Asian (EAS) AF: 0.512 AC: 2636 AN: 5148

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4820

European-Finnish (FIN) AF: 0.280 AC: 2960 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20946 AN: 67966

Other (OTH) AF: 0.281 AC: 593 AN: 2114

Alfa AF: 0.152 Hom.: 309

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7379332; hg19: chr5-55589175; COSMIC: COSV66155398;