11-4094257-T-C

Variant names:

• chr11-4094257-T-C
• rs11030918

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.303 in 152,092 control chromosomes in the GnomAD database, including 7,333 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 0.30 (7333 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 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: 0.303 AC: 46094 AN: 151974 Hom.: 7328 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.303 AC: 46119 AN: 152092 Hom.: 7333 Cov.: 33 AF XY: 0.309 AC XY: 22946 AN XY: 74330

African (AFR) AF: 0.215 AC: 8913 AN: 41500

American (AMR) AF: 0.269 AC: 4120 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1083 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5164

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4816

European-Finnish (FIN) AF: 0.396 AC: 4176 AN: 10552

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23240 AN: 67974

Other (OTH) AF: 0.281 AC: 594 AN: 2116

Alfa AF: 0.324 Hom.: 15092

Bravo AF: 0.280

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.58
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11030918; hg19: chr11-4115487;