rs2070898

Variant names:

• chr4-99322140-G-A
• rs2070898

Your query was ambiguous. Multiple possible variants found:

• chr4-99322140-G-A
• chr4-99322140-G-T

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 0.233 in 152,132 control chromosomes in the GnomAD database, including 5,586 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 0.23 (5586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.234 AC: 35509 AN: 152014 Hom.: 5595 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.233 AC: 35490 AN: 152132 Hom.: 5586 Cov.: 32 AF XY: 0.237 AC XY: 17632 AN XY: 74374

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.239

Alfa AF: 0.250 Hom.: 648

Bravo AF: 0.223

Asia WGS AF: 0.474 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070898; hg19: chr4-100243297;