rs11938795

Positions:

• chr4-122151854-T-C

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 0.24 in 152,188 control chromosomes in the GnomAD database, including 4,773 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 0.24 (4773 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36517 AN: 152070 Hom.: 4774 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.240 AC: 36533 AN: 152188 Hom.: 4773 Cov.: 33 AF XY: 0.230 AC XY: 17122 AN XY: 74430

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.248

Alfa AF: 0.244 Hom.: 6054

Bravo AF: 0.249

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11938795; hg19: chr4-123073009;