chr11-38423218-T-C

Variant names:

• chr11-38423218-T-C
• rs7938730

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 0.369 in 151,966 control chromosomes in the GnomAD database, including 12,100 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 0.37 (12100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 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: 0.369 AC: 56073 AN: 151848 Hom.: 12098 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.369 AC: 56084 AN: 151966 Hom.: 12100 Cov.: 32 AF XY: 0.362 AC XY: 26851 AN XY: 74264

African (AFR) AF: 0.211 AC: 8736 AN: 41446

American (AMR) AF: 0.286 AC: 4361 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1374 AN: 3464

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5164

South Asian (SAS) AF: 0.221 AC: 1064 AN: 4814

European-Finnish (FIN) AF: 0.471 AC: 4969 AN: 10552

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34089 AN: 67942

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.450 Hom.: 9399

Bravo AF: 0.347

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7938730; hg19: chr11-38444768;