rs1031724

Variant names:

• chr18-75815594-G-C
• rs1031724

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 0.0518 in 152,202 control chromosomes in the GnomAD database, including 496 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 0.052 (496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.0518 AC: 7874 AN: 152084 Hom.: 495 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0518 AC: 7891 AN: 152202 Hom.: 496 Cov.: 33 AF XY: 0.0512 AC XY: 3809 AN XY: 74420

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.00791

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0337 Hom.: 41

Bravo AF: 0.0572

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	18
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031724; hg19: chr18-73527549;