5-13214740-C-T

Variant names:

• chr5-13214740-C-T
• rs28207

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 0.323 in 151,872 control chromosomes in the GnomAD database, including 8,449 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 0.32 (8449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48965 AN: 151756 Hom.: 8444 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.323 AC: 48994 AN: 151872 Hom.: 8449 Cov.: 32 AF XY: 0.321 AC XY: 23858 AN XY: 74214

African (AFR) AF: 0.207 AC: 8578 AN: 41464

American (AMR) AF: 0.372 AC: 5677 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3468

East Asian (EAS) AF: 0.156 AC: 802 AN: 5154

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3578 AN: 10530

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26431 AN: 67880

Other (OTH) AF: 0.321 AC: 676 AN: 2106

Alfa AF: 0.352 Hom.: 4847

Bravo AF: 0.319

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.92
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs28207; hg19: chr5-13214852;