rs1020410

Variant names:

• chr2-175919410-T-C
• rs1020410

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 0.345 in 152,066 control chromosomes in the GnomAD database, including 9,579 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 0.34 (9579 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 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: 0.345 AC: 52397 AN: 151948 Hom.: 9579 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.345 AC: 52426 AN: 152066 Hom.: 9579 Cov.: 32 AF XY: 0.347 AC XY: 25788 AN XY: 74348

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.321

Alfa AF: 0.314 Hom.: 10780

Bravo AF: 0.345

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1020410; hg19: chr2-176784138;