chr9-77649668-C-T

Variant names:

• chr9-77649668-C-T
• rs11145506

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 0.0632 in 152,186 control chromosomes in the GnomAD database, including 656 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 0.063 (656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9612 AN: 152068 Hom.: 654 Cov.: 33

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0632 AC: 9611 AN: 152186 Hom.: 656 Cov.: 33 AF XY: 0.0711 AC XY: 5289 AN XY: 74402

African (AFR) AF: 0.0726 AC: 3013 AN: 41524

American (AMR) AF: 0.143 AC: 2191 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1318 AN: 5174

South Asian (SAS) AF: 0.136 AC: 655 AN: 4814

European-Finnish (FIN) AF: 0.112 AC: 1182 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1042 AN: 68020

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0335 Hom.: 824

Bravo AF: 0.0672

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.66
DANN	Benign	0.56
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11145506; hg19: chr9-80264584;