5-119447035-T-C

Variant names:

• chr5-119447035-T-C
• rs32646

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.306 in 152,076 control chromosomes in the GnomAD database, including 8,761 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 0.31 (8761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 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: 0.306 AC: 46507 AN: 151958 Hom.: 8754 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.306 AC: 46515 AN: 152076 Hom.: 8761 Cov.: 32 AF XY: 0.307 AC XY: 22837 AN XY: 74302

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.341

Alfa AF: 0.224 Hom.: 562

Bravo AF: 0.299

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32646; hg19: chr5-118782730;