2-19745816-T-C

Variant names:

• chr2-19745816-T-C
• rs2123536

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.829 in 152,136 control chromosomes in the GnomAD database, including 53,826 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 0.83 (53826 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 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: 0.829 AC: 126085 AN: 152018 Hom.: 53791 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.829 AC: 126177 AN: 152136 Hom.: 53826 Cov.: 33 AF XY: 0.825 AC XY: 61352 AN XY: 74380

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.845

Alfa AF: 0.918 Hom.: 44819

Bravo AF: 0.811

Asia WGS AF: 0.709 AC: 2466 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	0.13
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2123536; hg19: chr2-19945577;