chr11-76258589-G-T

Variant names:

• chr11-76258589-G-T
• rs12807555

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 0.126 in 152,180 control chromosomes in the GnomAD database, including 1,305 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 0.13 (1305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.126 AC: 19161 AN: 152062 Hom.: 1302 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0275

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0632

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.126 AC: 19181 AN: 152180 Hom.: 1305 Cov.: 32 AF XY: 0.123 AC XY: 9149 AN XY: 74422

African (AFR) AF: 0.143 AC: 5935 AN: 41488

American (AMR) AF: 0.113 AC: 1722 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 644 AN: 3472

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5180

South Asian (SAS) AF: 0.195 AC: 939 AN: 4820

European-Finnish (FIN) AF: 0.0632 AC: 670 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8744 AN: 68010

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.128 Hom.: 3218

Bravo AF: 0.127

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.9
DANN	Benign	0.68
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12807555; hg19: chr11-75969633;