chr4-130866627-A-C

Variant names:

• chr4-130866627-A-C
• rs2035213

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.796 AC: 32948 AN: 41384

American (AMR) AF: 0.928 AC: 14172 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3230 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4912 AN: 5106

South Asian (SAS) AF: 0.890 AC: 4281 AN: 4810

European-Finnish (FIN) AF: 0.938 AC: 9917 AN: 10576

Middle Eastern (MID) AF: 0.897 AC: 262 AN: 292

European-Non Finnish (NFE) AF: 0.935 AC: 63566 AN: 67972

Other (OTH) AF: 0.892 AC: 1880 AN: 2108

Alfa AF: 0.920 Hom.: 199250

Bravo AF: 0.891

Asia WGS AF: 0.905 AC: 3144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.88
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2035213; hg19: chr4-131787782;