rs11938968

Variant names:

• chr4-110821596-G-A
• rs11938968

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;