2-85496980-C-A

Position:

• chr2-85496980-C-A

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 0.193 in 152,018 control chromosomes in the GnomAD database, including 3,076 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 (3076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29346 AN: 151900 Hom.: 3072 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.193 AC: 29370 AN: 152018 Hom.: 3076 Cov.: 31 AF XY: 0.192 AC XY: 14242 AN XY: 74296

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.0856

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.202

Alfa AF: 0.173 Hom.: 616

Bravo AF: 0.184

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72844414; hg19: chr2-85724103;