rs10830236

Variant names:

• chr11-89167648-C-T
• rs10830236

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 0.268 in 151,796 control chromosomes in the GnomAD database, including 5,746 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 0.27 (5746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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: 0.268 AC: 40592 AN: 151678 Hom.: 5743 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.268 AC: 40615 AN: 151796 Hom.: 5746 Cov.: 32 AF XY: 0.266 AC XY: 19722 AN XY: 74182

African (AFR) AF: 0.189 AC: 7846 AN: 41414

American (AMR) AF: 0.231 AC: 3516 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1067 AN: 5124

South Asian (SAS) AF: 0.162 AC: 781 AN: 4818

European-Finnish (FIN) AF: 0.324 AC: 3417 AN: 10552

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22196 AN: 67878

Other (OTH) AF: 0.264 AC: 557 AN: 2110

Alfa AF: 0.302 Hom.: 30141

Bravo AF: 0.257

Asia WGS AF: 0.189 AC: 656 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.19
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10830236; hg19: chr11-88900816;