5-101365896-C-T

Variant names:

• chr5-101365896-C-T
• rs12153327

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 0.418 in 151,990 control chromosomes in the GnomAD database, including 15,273 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 0.42 (15273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.418 AC: 63497 AN: 151870 Hom.: 15273 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.418 AC: 63502 AN: 151990 Hom.: 15273 Cov.: 32 AF XY: 0.412 AC XY: 30580 AN XY: 74292

African (AFR) AF: 0.203 AC: 8429 AN: 41454

American (AMR) AF: 0.387 AC: 5912 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1720 AN: 3464

East Asian (EAS) AF: 0.150 AC: 772 AN: 5160

South Asian (SAS) AF: 0.354 AC: 1704 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5382 AN: 10546

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38028 AN: 67962

Other (OTH) AF: 0.430 AC: 910 AN: 2114

Alfa AF: 0.500 Hom.: 79425

Bravo AF: 0.397

Asia WGS AF: 0.259 AC: 902 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	0.26
DANN	Benign	0.62
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs12153327; hg19: chr5-100701600;