5-83724319-T-C

Variant names:

• chr5-83724319-T-C
• rs975563

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 0.345 in 152,040 control chromosomes in the GnomAD database, including 9,211 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 0.35 (9211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.345 AC: 52442 AN: 151920 Hom.: 9201 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.345 AC: 52471 AN: 152040 Hom.: 9211 Cov.: 32 AF XY: 0.344 AC XY: 25558 AN XY: 74308

African (AFR) AF: 0.334 AC: 13857 AN: 41486

American (AMR) AF: 0.291 AC: 4455 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5160

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3376 AN: 10546

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24832 AN: 67960

Other (OTH) AF: 0.325 AC: 685 AN: 2106

Alfa AF: 0.357 Hom.: 31484

Bravo AF: 0.342

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs975563; hg19: chr5-83020138;