2-85582866-C-T

Variant names:

• chr2-85582866-C-T
• rs1561198

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 0.514 in 152,076 control chromosomes in the GnomAD database, including 21,120 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 0.51 (21120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -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 = 0.684 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: 0.513 AC: 78027 AN: 151958 Hom.: 21083 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.514 AC: 78119 AN: 152076 Hom.: 21120 Cov.: 32 AF XY: 0.509 AC XY: 37857 AN XY: 74328

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.498

Alfa AF: 0.462 Hom.: 23113

Bravo AF: 0.518

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561198; hg19: chr2-85809989;