5-83724319-T-C

Variant names:

• chr5-83724319-T-C
• rs975563

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.345 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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.325

Alfa AF: 0.349 Hom.: 11134

Bravo AF: 0.342

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs975563; hg19: chr5-83020138;