2-145550546-A-C

Variant names:

• chr2-145550546-A-C
• rs10496982

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 0.14 in 151,798 control chromosomes in the GnomAD database, including 2,273 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 0.14 (2273 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.140 AC: 21273 AN: 151680 Hom.: 2270 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 151798 Hom.: 2273 Cov.: 31 AF XY: 0.141 AC XY: 10490 AN XY: 74196

African (AFR) AF: 0.287 AC: 11872 AN: 41402

American (AMR) AF: 0.111 AC: 1695 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 331 AN: 3458

East Asian (EAS) AF: 0.124 AC: 640 AN: 5150

South Asian (SAS) AF: 0.242 AC: 1165 AN: 4816

European-Finnish (FIN) AF: 0.0379 AC: 401 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4837 AN: 67852

Other (OTH) AF: 0.122 AC: 258 AN: 2108

Alfa AF: 0.0923 Hom.: 1324

Bravo AF: 0.148

Asia WGS AF: 0.188 AC: 651 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10496982; hg19: chr2-146308114;