rs11202308

Variant names:

• chr10-87039853-T-G
• rs11202308

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 0.113 in 152,266 control chromosomes in the GnomAD database, including 1,254 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 0.11 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 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: 0.113 AC: 17183 AN: 152148 Hom.: 1255 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.113 AC: 17172 AN: 152266 Hom.: 1254 Cov.: 32 AF XY: 0.113 AC XY: 8444 AN XY: 74458

African (AFR) AF: 0.0257 AC: 1069 AN: 41566

American (AMR) AF: 0.157 AC: 2401 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3470

East Asian (EAS) AF: 0.0665 AC: 345 AN: 5188

South Asian (SAS) AF: 0.143 AC: 689 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1466 AN: 10598

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9884 AN: 68018

Other (OTH) AF: 0.147 AC: 310 AN: 2116

Alfa AF: 0.129 Hom.: 1556

Bravo AF: 0.112

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11202308; hg19: chr10-88799610;