19-1102212-A-G

Variant names:

• chr19-1102212-A-G
• rs3746165

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 151,850 control chromosomes in the GnomAD database, including 21,968 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 (21968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 20 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 (AFR) allele frequency at 95% confidence interval = 0.587 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: 81355 AN: 151732 Hom.: 21932 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.536 AC: 81446 AN: 151850 Hom.: 21968 Cov.: 31 AF XY: 0.544 AC XY: 40399 AN XY: 74232

African (AFR) AF: 0.593 AC: 24541 AN: 41392

American (AMR) AF: 0.586 AC: 8938 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2829 AN: 5164

South Asian (SAS) AF: 0.551 AC: 2659 AN: 4824

European-Finnish (FIN) AF: 0.608 AC: 6387 AN: 10502

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

European-Non Finnish (NFE) AF: 0.479 AC: 32537 AN: 67926

Other (OTH) AF: 0.521 AC: 1101 AN: 2114

Alfa AF: 0.539 Hom.: 3910

Bravo AF: 0.534

Asia WGS AF: 0.580 AC: 2017 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	1.6
DANN	Benign	0.33
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs3746165; hg19: chr19-1102211;