rs11130605

Variant names:

• chr3-58003442-C-T
• rs11130605

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 0.335 in 152,010 control chromosomes in the GnomAD database, including 9,242 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 0.33 (9242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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: 0.335 AC: 50911 AN: 151892 Hom.: 9243 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.335 AC: 50920 AN: 152010 Hom.: 9242 Cov.: 31 AF XY: 0.333 AC XY: 24716 AN XY: 74282

African (AFR) AF: 0.268 AC: 11103 AN: 41462

American (AMR) AF: 0.280 AC: 4272 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3464

East Asian (EAS) AF: 0.00753 AC: 39 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4547 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26704 AN: 67968

Other (OTH) AF: 0.357 AC: 755 AN: 2112

Alfa AF: 0.374 Hom.: 46643

Bravo AF: 0.322

Asia WGS AF: 0.164 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.65
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11130605;

hg19: chr3-57989169;