rs11938968

chr4-110821596-G-A

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 0.416 in 151,992 control chromosomes in the GnomAD database, including 14,507 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 0.42 (14507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

ACMG classification

Verdict is Benign. Variant got -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 = 0.503 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: 0.416 AC: 63210 AN: 151872 Hom.: 14499 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.416 AC: 63231 AN: 151992 Hom.: 14507 Cov.: 32 AF XY: 0.420 AC XY: 31205 AN XY: 74270

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.396

Alfa AF: 0.487 Hom.: 10726

Bravo AF: 0.402

Asia WGS AF: 0.449 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11938968; hg19: chr4-111742752;