4-183519827-A-T

Variant names:

• chr4-183519827-A-T
• rs11735038

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 0.493 in 151,982 control chromosomes in the GnomAD database, including 20,220 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 0.49 (20220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.629 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: 0.493 AC: 74876 AN: 151864 Hom.: 20203 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.493 AC: 74948 AN: 151982 Hom.: 20220 Cov.: 32 AF XY: 0.483 AC XY: 35887 AN XY: 74282

African (AFR) AF: 0.306 AC: 12675 AN: 41428

American (AMR) AF: 0.478 AC: 7290 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3472

East Asian (EAS) AF: 0.182 AC: 940 AN: 5168

South Asian (SAS) AF: 0.470 AC: 2267 AN: 4824

European-Finnish (FIN) AF: 0.509 AC: 5366 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43077 AN: 67968

Other (OTH) AF: 0.501 AC: 1056 AN: 2106

Alfa AF: 0.461 Hom.: 1507

Bravo AF: 0.478

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.087
DANN	Benign	0.70
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11735038; hg19: chr4-184440980;