rs541458

Variant names:

• chr11-86077309-C-T
• rs541458

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 0.7 in 152,094 control chromosomes in the GnomAD database, including 37,620 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 0.70 (37620 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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: 0.700 AC: 106331 AN: 151976 Hom.: 37586 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.700 AC: 106421 AN: 152094 Hom.: 37620 Cov.: 31 AF XY: 0.693 AC XY: 51523 AN XY: 74340

African (AFR) AF: 0.796 AC: 33057 AN: 41512

American (AMR) AF: 0.657 AC: 10031 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2494 AN: 5172

South Asian (SAS) AF: 0.588 AC: 2833 AN: 4820

European-Finnish (FIN) AF: 0.648 AC: 6845 AN: 10556

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46735 AN: 67980

Other (OTH) AF: 0.689 AC: 1453 AN: 2108

Alfa AF: 0.686 Hom.: 25883

Bravo AF: 0.703

Asia WGS AF: 0.553 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs541458; hg19: chr11-85788351;