19-1107161-C-T

Variant names:

• chr19-1107161-C-T
• rs2074452

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 0.319 in 152,156 control chromosomes in the GnomAD database, including 8,225 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 0.32 (8225 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.319 AC: 48469 AN: 152038 Hom.: 8200 Cov.: 35

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.319 AC: 48553 AN: 152156 Hom.: 8225 Cov.: 35 AF XY: 0.321 AC XY: 23897 AN XY: 74382

African (AFR) AF: 0.436 AC: 18110 AN: 41490

American (AMR) AF: 0.260 AC: 3970 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1868 AN: 5172

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4820

European-Finnish (FIN) AF: 0.327 AC: 3471 AN: 10608

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17778 AN: 67986

Other (OTH) AF: 0.292 AC: 616 AN: 2112

Alfa AF: 0.284 Hom.: 1091

Bravo AF: 0.318

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2074452; hg19: chr19-1107160; COSMIC: COSV62322495;