2-78818795-C-G

Position:

• chr2-78818795-C-G

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 0.194 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.78818795C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.177

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496211; hg19: chr2-79045921;