chr19-1102115-G-C

Variant names:

• chr19-1102115-G-C
• rs757229

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 0.536 in 151,940 control chromosomes in the GnomAD database, including 21,941 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 0.54 (21941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 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: 0.536 AC: 81335 AN: 151820 Hom.: 21904 Cov.: 33

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.536 AC: 81428 AN: 151940 Hom.: 21941 Cov.: 33 AF XY: 0.544 AC XY: 40396 AN XY: 74274

African (AFR) AF: 0.593 AC: 24542 AN: 41420

American (AMR) AF: 0.586 AC: 8944 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2825 AN: 5158

South Asian (SAS) AF: 0.551 AC: 2658 AN: 4824

European-Finnish (FIN) AF: 0.607 AC: 6405 AN: 10544

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32508 AN: 67946

Other (OTH) AF: 0.520 AC: 1094 AN: 2102

Alfa AF: 0.390 Hom.: 1032

Bravo AF: 0.534

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs757229; hg19: chr19-1102114;