8-9549072-C-T

Variant names:

• chr8-9549072-C-T
• rs11991621

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 0.18 in 152,086 control chromosomes in the GnomAD database, including 2,678 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 0.18 (2678 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.180 AC: 27325 AN: 151968 Hom.: 2663 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.180 AC: 27369 AN: 152086 Hom.: 2678 Cov.: 33 AF XY: 0.182 AC XY: 13541 AN XY: 74318

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0950

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.154

Alfa AF: 0.156 Hom.: 1465

Bravo AF: 0.169

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11991621; hg19: chr8-9406582;