chr2-49797064-T-C

Variant names:

• chr2-49797064-T-C
• rs1878856

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 0.222 in 152,180 control chromosomes in the GnomAD database, including 4,127 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 0.22 (4127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.222 AC: 33749 AN: 152062 Hom.: 4129 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.222 AC: 33762 AN: 152180 Hom.: 4127 Cov.: 32 AF XY: 0.219 AC XY: 16289 AN XY: 74420

African (AFR) AF: 0.152 AC: 6328 AN: 41526

American (AMR) AF: 0.192 AC: 2930 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1063 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5178

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4828

European-Finnish (FIN) AF: 0.207 AC: 2192 AN: 10586

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18551 AN: 67984

Other (OTH) AF: 0.230 AC: 486 AN: 2114

Alfa AF: 0.260 Hom.: 6489

Bravo AF: 0.213

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1878856; hg19: chr2-50024202;