11-45842591-T-A

Variant names:

• chr11-45842591-T-A
• rs7121611

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 0.397 in 152,122 control chromosomes in the GnomAD database, including 14,517 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 0.40 (14517 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.397 AC: 60362 AN: 152004 Hom.: 14508 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.397 AC: 60385 AN: 152122 Hom.: 14517 Cov.: 33 AF XY: 0.399 AC XY: 29665 AN XY: 74356

African (AFR) AF: 0.124 AC: 5141 AN: 41524

American (AMR) AF: 0.500 AC: 7631 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2449 AN: 4824

European-Finnish (FIN) AF: 0.475 AC: 5021 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35336 AN: 67986

Other (OTH) AF: 0.435 AC: 919 AN: 2114

Alfa AF: 0.450 Hom.: 2103

Bravo AF: 0.386

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs7121611; hg19: chr11-45864142;