rs10895304

Variant names:

• chr11-102519261-A-G
• rs10895304

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 0.202 in 152,132 control chromosomes in the GnomAD database, including 3,316 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 0.20 (3316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.267 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: 0.202 AC: 30749 AN: 152014 Hom.: 3315 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.202 AC: 30764 AN: 152132 Hom.: 3316 Cov.: 32 AF XY: 0.201 AC XY: 14962 AN XY: 74384

African (AFR) AF: 0.241 AC: 9990 AN: 41462

American (AMR) AF: 0.240 AC: 3666 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1446 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10610

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11909 AN: 67992

Other (OTH) AF: 0.230 AC: 486 AN: 2112

Alfa AF: 0.191 Hom.: 5514

Bravo AF: 0.213

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.28
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10895304; hg19: chr11-102389992;