rs555875

Positions:

• chr11-75364284-T-C
• chr11-75364284-T-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.75364284T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.409

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs555875; hg19: chr11-75075328;