chr5-63258773-C-T

Position:

• chr5-63258773-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 0.0332 in 152,246 control chromosomes in the GnomAD database, including 141 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 0.033 (141 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0332 (5057/152246) while in subpopulation NFE AF= 0.05 (3404/68014). AF 95% confidence interval is 0.0486. There are 141 homozygotes in gnomad4. There are 2444 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 141 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: 0.0332 AC: 5056 AN: 152128 Hom.: 141 Cov.: 33

Gnomad AFR AF: 0.00878

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0332 AC: 5057 AN: 152246 Hom.: 141 Cov.: 33 AF XY: 0.0328 AC XY: 2444 AN XY: 74426

Gnomad4 AFR AF: 0.00878

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0500

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0463 Hom.: 30

Bravo AF: 0.0292

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10042956; hg19: chr5-62554600;