11-69728315-C-T

Variant names:

• chr11-69728315-C-T
• rs7115260

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 0.208 in 152,066 control chromosomes in the GnomAD database, including 3,473 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 0.21 (3473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.208 AC: 31662 AN: 151950 Hom.: 3467 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152066 Hom.: 3473 Cov.: 32 AF XY: 0.207 AC XY: 15378 AN XY: 74342

African (AFR) AF: 0.267 AC: 11063 AN: 41440

American (AMR) AF: 0.140 AC: 2143 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3468

East Asian (EAS) AF: 0.0563 AC: 291 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4816

European-Finnish (FIN) AF: 0.202 AC: 2140 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13830 AN: 67982

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.203 Hom.: 6119

Bravo AF: 0.203

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.51
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7115260; hg19: chr11-69543083;