rs10896468

Variant names:

• chr11-56509110-G-T
• rs10896468

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 0.173 in 152,122 control chromosomes in the GnomAD database, including 2,679 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 0.17 (2679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 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: 0.173 AC: 26310 AN: 152004 Hom.: 2680 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.173 AC: 26304 AN: 152122 Hom.: 2679 Cov.: 32 AF XY: 0.171 AC XY: 12746 AN XY: 74356

African (AFR) AF: 0.0615 AC: 2555 AN: 41512

American (AMR) AF: 0.153 AC: 2337 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 946 AN: 3472

East Asian (EAS) AF: 0.132 AC: 685 AN: 5178

South Asian (SAS) AF: 0.174 AC: 838 AN: 4814

European-Finnish (FIN) AF: 0.212 AC: 2239 AN: 10564

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15971 AN: 67984

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.190 Hom.: 454

Bravo AF: 0.163

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.54
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10896468; hg19: chr11-56276586;