rs1978423

Variant names:

• chr19-18339903-T-C
• rs1978423

Your query was ambiguous. Multiple possible variants found:

• chr19-18339903-T-C
• chr19-18339903-T-G

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 0.0927 in 152,022 control chromosomes in the GnomAD database, including 919 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 0.093 (919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.0927 AC: 14081 AN: 151904 Hom.: 917 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0985

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0927 AC: 14085 AN: 152022 Hom.: 919 Cov.: 32 AF XY: 0.0931 AC XY: 6922 AN XY: 74312

Gnomad4 AFR AF: 0.0272

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.115 Hom.: 1681

Bravo AF: 0.0803

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978423; hg19: chr19-18450713;