11-9534570-T-C

Variant names:

• chr11-9534570-T-C
• rs7102407

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 0.172 in 152,140 control chromosomes in the GnomAD database, including 3,587 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 0.17 (3587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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: 0.172 AC: 26079 AN: 152022 Hom.: 3566 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.172 AC: 26135 AN: 152140 Hom.: 3587 Cov.: 31 AF XY: 0.167 AC XY: 12444 AN XY: 74390

African (AFR) AF: 0.381 AC: 15819 AN: 41470

American (AMR) AF: 0.0929 AC: 1419 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4828

European-Finnish (FIN) AF: 0.0865 AC: 916 AN: 10584

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6783 AN: 68006

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.107 Hom.: 2337

Bravo AF: 0.184

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.43
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs7102407; hg19: chr11-9556117;