rs4937100

Positions:

• chr11-112143063-A-G

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 0.376 in 151,776 control chromosomes in the GnomAD database, including 11,028 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 0.38 (11028 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 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: 0.376 AC: 57007 AN: 151660 Hom.: 11002 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.376 AC: 57072 AN: 151776 Hom.: 11028 Cov.: 33 AF XY: 0.379 AC XY: 28081 AN XY: 74190

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.403

Alfa AF: 0.351 Hom.: 1202

Bravo AF: 0.380

Asia WGS AF: 0.547 AC: 1863 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4937100; hg19: chr11-112013786;