5-132064740-T-C

Variant names:

• chr5-132064740-T-C
• rs2069803

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 0.333 in 152,006 control chromosomes in the GnomAD database, including 9,196 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 0.33 (9196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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: 0.333 AC: 50568 AN: 151888 Hom.: 9191 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.333 AC: 50582 AN: 152006 Hom.: 9196 Cov.: 32 AF XY: 0.318 AC XY: 23631 AN XY: 74292

African (AFR) AF: 0.281 AC: 11637 AN: 41466

American (AMR) AF: 0.316 AC: 4830 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3472

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5168

South Asian (SAS) AF: 0.112 AC: 539 AN: 4818

European-Finnish (FIN) AF: 0.269 AC: 2845 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28234 AN: 67910

Other (OTH) AF: 0.354 AC: 747 AN: 2112

Alfa AF: 0.231 Hom.: 522

Bravo AF: 0.338

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.8
DANN	Benign	0.82
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs2069803; hg19: chr5-131400433; COSMIC: COSV57308668;