rs1073981

Variant names:

• chr2-66782579-G-A
• rs1073981

Your query was ambiguous. Multiple possible variants found:

• chr2-66782579-G-A
• chr2-66782579-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 0.035 in 152,186 control chromosomes in the GnomAD database, including 226 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 0.035 (226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 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: 0.0350 AC: 5316 AN: 152068 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.00780

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0350 AC: 5329 AN: 152186 Hom.: 226 Cov.: 32 AF XY: 0.0404 AC XY: 3004 AN XY: 74390

Gnomad4 AFR AF: 0.00782

Gnomad4 AMR AF: 0.0946

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.0808

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.00895 Hom.: 2

Bravo AF: 0.0358

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073981; hg19: chr2-67009711;