chr5-132673907-C-T

Position:

• chr5-132673907-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00432 in 830,508 control chromosomes in the GnomAD database, including 58 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 0.0046 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0042 (49 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00464 (706/152184) while in subpopulation EAS AF= 0.0228 (118/5182). AF 95% confidence interval is 0.0194. There are 9 homozygotes in gnomad4. There are 475 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00464 AC: 706 AN: 152066 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00851

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00104

Gnomad OTH AF: 0.00287

GnomAD4 exome AF: 0.00425 AC: 2882 AN: 678324 Hom.: 49 AF XY: 0.00398 AC XY: 1390 AN XY: 349290

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.0228

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0149

Gnomad4 SAS exome AF: 0.000655

Gnomad4 FIN exome AF: 0.0364

Gnomad4 NFE exome AF: 0.000609

Gnomad4 OTH exome AF: 0.00479

GnomAD4 genome AF: 0.00464 AC: 706 AN: 152184 Hom.: 9 Cov.: 32 AF XY: 0.00638 AC XY: 475 AN XY: 74400

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.00857

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.00106

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00530 Hom.: 7

Bravo AF: 0.00326

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	13
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17772853; hg19: chr5-132009599;