rs11465996

chr8-73989727-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.25 in 152,014 control chromosomes in the GnomAD database, including 5,085 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 0.25 (5085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

ACMG classification

Verdict is Benign. Variant got -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 = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37974 AN: 151894 Hom.: 5084 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.250 AC: 37983 AN: 152014 Hom.: 5085 Cov.: 32 AF XY: 0.251 AC XY: 18628 AN XY: 74312

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.228

Alfa AF: 0.269 Hom.: 739

Bravo AF: 0.239

Asia WGS AF: 0.240 AC: 836 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	7.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11465996; hg19: chr8-74901962;