chr4-73540998-A-T

Variant names:

• chr4-73540998-A-T
• rs10518115

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 0.2 in 152,160 control chromosomes in the GnomAD database, including 3,780 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 0.20 (3780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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: 0.200 AC: 30367 AN: 152046 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.200 AC: 30384 AN: 152160 Hom.: 3780 Cov.: 32 AF XY: 0.202 AC XY: 15053 AN XY: 74368

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.246

Alfa AF: 0.215 Hom.: 466

Bravo AF: 0.202

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518115; hg19: chr4-74406715;