chr2-19383014-T-C

Variant names:

• chr2-19383014-T-C
• rs7603289

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 0.265 in 151,980 control chromosomes in the GnomAD database, including 5,779 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 0.27 (5779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.266 AC: 40324 AN: 151862 Hom.: 5778 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40332 AN: 151980 Hom.: 5779 Cov.: 32 AF XY: 0.257 AC XY: 19114 AN XY: 74306

African (AFR) AF: 0.246 AC: 10195 AN: 41480

American (AMR) AF: 0.205 AC: 3136 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3470

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5168

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4822

European-Finnish (FIN) AF: 0.227 AC: 2389 AN: 10544

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21510 AN: 67920

Other (OTH) AF: 0.261 AC: 550 AN: 2106

Alfa AF: 0.276 Hom.: 2647

Bravo AF: 0.265

Asia WGS AF: 0.122 AC: 427 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7603289; hg19: chr2-19582775;