19-40983099-G-C

Variant names:

• chr19-40983099-G-C
• rs11083595

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 0.289 in 151,836 control chromosomes in the GnomAD database, including 6,889 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 0.29 (6889 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.289 AC: 43808 AN: 151718 Hom.: 6886 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.289 AC: 43824 AN: 151836 Hom.: 6889 Cov.: 31 AF XY: 0.288 AC XY: 21386 AN XY: 74212

African (AFR) AF: 0.384 AC: 15846 AN: 41294

American (AMR) AF: 0.343 AC: 5230 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5162

South Asian (SAS) AF: 0.382 AC: 1829 AN: 4782

European-Finnish (FIN) AF: 0.182 AC: 1932 AN: 10600

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16080 AN: 67958

Other (OTH) AF: 0.305 AC: 644 AN: 2112

Alfa AF: 0.112 Hom.: 163

Bravo AF: 0.301

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.80
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs11083595; hg19: chr19-41489004; COSMIC: COSV62488846;