2-78818795-C-G

Variant names:

• chr2-78818795-C-G
• rs10496211

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 0.194 in 152,092 control chromosomes in the GnomAD database, including 2,958 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 0.19 (2958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.194 AC: 29498 AN: 151974 Hom.: 2951 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.194 AC: 29528 AN: 152092 Hom.: 2958 Cov.: 32 AF XY: 0.196 AC XY: 14560 AN XY: 74340

African (AFR) AF: 0.157 AC: 6519 AN: 41478

American (AMR) AF: 0.191 AC: 2924 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.105 AC: 543 AN: 5178

South Asian (SAS) AF: 0.149 AC: 720 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2922 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14910 AN: 67984

Other (OTH) AF: 0.177 AC: 373 AN: 2104

Alfa AF: 0.123 Hom.: 209

Bravo AF: 0.189

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.45
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10496211; hg19: chr2-79045921;