rs2035213

Positions:

• chr4-130866627-A-C
• chr4-130866627-A-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 0.895 in 151,900 control chromosomes in the GnomAD database, including 61,232 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 0.90 (61232 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.896 AC: 135924 AN: 151782 Hom.: 61189 Cov.: 29

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.895 AC: 136022 AN: 151900 Hom.: 61232 Cov.: 29 AF XY: 0.896 AC XY: 66524 AN XY: 74224

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.892

Alfa AF: 0.927 Hom.: 129125

Bravo AF: 0.891

Asia WGS AF: 0.905 AC: 3144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035213; hg19: chr4-131787782;