rs1030874

Variant names:

• chr2-210965193-C-G
• rs1030874

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 0.609 in 151,894 control chromosomes in the GnomAD database, including 29,409 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 0.61 (29409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.609 AC: 92456 AN: 151776 Hom.: 29390 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.609 AC: 92516 AN: 151894 Hom.: 29409 Cov.: 32 AF XY: 0.616 AC XY: 45751 AN XY: 74248

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.604

Alfa AF: 0.611 Hom.: 3108

Bravo AF: 0.602

Asia WGS AF: 0.857 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1030874; hg19: chr2-211829917;