11-75364284-T-C

Variant names:

• chr11-75364284-T-C
• rs555875

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 0.395 in 148,354 control chromosomes in the GnomAD database, including 11,841 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 0.39 (11841 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.395 AC: 58511 AN: 148256 Hom.: 11812 Cov.: 30

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.395 AC: 58587 AN: 148354 Hom.: 11841 Cov.: 30 AF XY: 0.382 AC XY: 27601 AN XY: 72274

African (AFR) AF: 0.424 AC: 17004 AN: 40084

American (AMR) AF: 0.326 AC: 4867 AN: 14934

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1269 AN: 3438

East Asian (EAS) AF: 0.164 AC: 823 AN: 5018

South Asian (SAS) AF: 0.187 AC: 863 AN: 4622

European-Finnish (FIN) AF: 0.330 AC: 3225 AN: 9772

Middle Eastern (MID) AF: 0.392 AC: 113 AN: 288

European-Non Finnish (NFE) AF: 0.436 AC: 29327 AN: 67228

Other (OTH) AF: 0.409 AC: 850 AN: 2080

Alfa AF: 0.401 Hom.: 1556

Bravo AF: 0.391

Asia WGS AF: 0.200 AC: 682 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs555875; hg19: chr11-75075328;