11-270715-T-C

Position:

• chr11-270715-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 0.192 in 152,040 control chromosomes in the GnomAD database, including 3,278 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 0.19 (3278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.192 AC: 29239 AN: 151922 Hom.: 3276 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.192 AC: 29256 AN: 152040 Hom.: 3278 Cov.: 32 AF XY: 0.197 AC XY: 14651 AN XY: 74332

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.189

Alfa AF: 0.216 Hom.: 2451

Bravo AF: 0.180

Asia WGS AF: 0.0590 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17655730; hg19: chr11-270715;