7-128935743-TCTTAGCTATTGCTC-T

Variant names:

• chr7-128935743-TCTTAGCTATTGCTC-T
• rs11269962

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11600 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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: 0.377 AC: 57271 AN: 151968 Hom.: 11602 Cov.: 0

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.377 AC: 57288 AN: 152086 Hom.: 11600 Cov.: 0 AF XY: 0.372 AC XY: 27678 AN XY: 74328

African (AFR) AF: 0.260 AC: 10783 AN: 41506

American (AMR) AF: 0.404 AC: 6183 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3468

East Asian (EAS) AF: 0.122 AC: 635 AN: 5188

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4249 AN: 10578

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30280 AN: 67924

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.404 Hom.: 1550

Bravo AF: 0.373

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs11269962; hg19: chr7-128575797;