rs2980089

Variant names:

• chr4-4265571-G-A
• rs2980089

Your query was ambiguous. Multiple possible variants found:

• chr4-4265571-G-A
• chr4-4265571-G-C
• chr4-4265571-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 0.611 in 152,094 control chromosomes in the GnomAD database, including 29,346 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 (29346 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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 (NFE) allele frequency at 95% confidence interval = 0.699 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: 0.611 AC: 92834 AN: 151976 Hom.: 29328 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.611 AC: 92897 AN: 152094 Hom.: 29346 Cov.: 33 AF XY: 0.604 AC XY: 44900 AN XY: 74354

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.606

Alfa AF: 0.675 Hom.: 57003

Bravo AF: 0.597

Asia WGS AF: 0.455 AC: 1583 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	4.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980089; hg19: chr4-4267298;