rs873108

Variant names:

• chr11-76744574-C-T
• rs873108

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 0.221 in 152,040 control chromosomes in the GnomAD database, including 4,063 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 0.22 (4063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.221 AC: 33531 AN: 151922 Hom.: 4054 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.221 AC: 33580 AN: 152040 Hom.: 4063 Cov.: 32 AF XY: 0.224 AC XY: 16649 AN XY: 74332

African (AFR) AF: 0.287 AC: 11886 AN: 41444

American (AMR) AF: 0.216 AC: 3296 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1847 AN: 5166

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4820

European-Finnish (FIN) AF: 0.179 AC: 1893 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11521 AN: 67972

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.193 Hom.: 5107

Bravo AF: 0.227

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.1
DANN	Benign	0.83
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs873108; hg19: chr11-76455618;