rs1818976

chr19-24247689-G-Cchr19-24247689-G-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 0.14 in 151,516 control chromosomes in the GnomAD database, including 2,385 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 0.14 (2385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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: 0.140 AC: 21145 AN: 151398 Hom.: 2378 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0656

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.140 AC: 21189 AN: 151516 Hom.: 2385 Cov.: 32 AF XY: 0.139 AC XY: 10266 AN XY: 74028

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0656

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0298 Hom.: 24

Bravo AF: 0.155

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1818976; hg19: chr19-24430491;