11-7235910-C-T

Variant names:

• chr11-7235910-C-T
• rs1552462

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 0.0283 in 152,178 control chromosomes in the GnomAD database, including 128 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 0.028 (128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 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: 0.0284 AC: 4314 AN: 152060 Hom.: 128 Cov.: 32

Gnomad AFR AF: 0.00655

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0283 AC: 4313 AN: 152178 Hom.: 128 Cov.: 32 AF XY: 0.0317 AC XY: 2358 AN XY: 74386

African (AFR) AF: 0.00650 AC: 270 AN: 41524

American (AMR) AF: 0.0732 AC: 1117 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.123 AC: 634 AN: 5164

South Asian (SAS) AF: 0.0261 AC: 126 AN: 4828

European-Finnish (FIN) AF: 0.0439 AC: 465 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0229 AC: 1560 AN: 68006

Other (OTH) AF: 0.0270 AC: 57 AN: 2114

Alfa AF: 0.0231 Hom.: 114

Bravo AF: 0.0299

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1552462; hg19: chr11-7257141;