chr19-9193409-T-C

Variant names:

• chr19-9193409-T-C
• rs878246

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 0.225 in 152,144 control chromosomes in the GnomAD database, including 3,957 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 0.22 (3957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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: 0.225 AC: 34217 AN: 152026 Hom.: 3961 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.225 AC: 34216 AN: 152144 Hom.: 3957 Cov.: 32 AF XY: 0.228 AC XY: 16963 AN XY: 74364

African (AFR) AF: 0.218 AC: 9065 AN: 41522

American (AMR) AF: 0.180 AC: 2749 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 970 AN: 3456

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5174

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4816

European-Finnish (FIN) AF: 0.271 AC: 2871 AN: 10576

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15176 AN: 68008

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.224 Hom.: 1364

Bravo AF: 0.215

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs878246; hg19: chr19-9304085;