2-105236375-A-G

Variant names:

• chr2-105236375-A-G
• rs1545122

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 0.831 in 152,130 control chromosomes in the GnomAD database, including 52,794 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 (52794 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.831 AC: 126316 AN: 152012 Hom.: 52749 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.831 AC: 126416 AN: 152130 Hom.: 52794 Cov.: 31 AF XY: 0.830 AC XY: 61726 AN XY: 74352

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.829

Alfa AF: 0.822 Hom.: 67628

Bravo AF: 0.841

Asia WGS AF: 0.942 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	15
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1545122; hg19: chr2-105852832; COSMIC: COSV60087780;