11-45843381-T-G

Variant names:

• chr11-45843381-T-G
• rs61884508

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.024 in 152,270 control chromosomes in the GnomAD database, including 77 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 0.024 (77 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.024 (3651/152270) while in subpopulation NFE AF = 0.0357 (2429/68002). AF 95% confidence interval is 0.0345. There are 77 homozygotes in GnomAd4. There are 1686 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 77 gene

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: 0.0240 AC: 3654 AN: 152152 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.00661

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0285

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0240 AC: 3651 AN: 152270 Hom.: 77 Cov.: 32 AF XY: 0.0226 AC XY: 1686 AN XY: 74452

African (AFR) AF: 0.00659 AC: 274 AN: 41562

American (AMR) AF: 0.0283 AC: 433 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4822

European-Finnish (FIN) AF: 0.0128 AC: 136 AN: 10616

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2429 AN: 68002

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0327 Hom.: 16

Bravo AF: 0.0243

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs61884508; hg19: chr11-45864932;