rs4245232

chr18-49560628-A-Cchr18-49560628-A-T

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 0.824 in 152,260 control chromosomes in the GnomAD database, including 52,628 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 0.82 (52618 hom., cov: 33)
  • Exomes 𝑓: 0.91 (10 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

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 (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125320 AN: 152120 Hom.: 52566 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.933

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.842

GnomAD4 exome AF: 0.909 AC: 20 AN: 22 Hom.: 10 AF XY: 0.833 AC XY: 10 AN XY: 12

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.857

GnomAD4 genome AF: 0.824 AC: 125422 AN: 152238 Hom.: 52618 Cov.: 33 AF XY: 0.818 AC XY: 60842 AN XY: 74414

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.844

Alfa AF: 0.814 Hom.: 79493

Bravo AF: 0.821

Asia WGS AF: 0.723 AC: 2513 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	8.6
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4245232; hg19: chr18-47086998;