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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0272 AC: 1129 AN: 41482

American (AMR) AF: 0.0638 AC: 975 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5172

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2149 AN: 10562

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9017 AN: 67928

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.113 Hom.: 2432

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1978423; hg19: chr19-18450713;