11-4274989-G-C

Position:

• chr11-4274989-G-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 0.108 in 147,510 control chromosomes in the GnomAD database, including 2,208 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 0.11 (2208 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.108 AC: 15913 AN: 147412 Hom.: 2210 Cov.: 29

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.108 AC: 15900 AN: 147510 Hom.: 2208 Cov.: 29 AF XY: 0.106 AC XY: 7646 AN XY: 71888

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0374 Hom.: 70

Asia WGS AF: 0.193 AC: 638 AN: 3316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031481; hg19: chr11-4296219;