chr9-81880693-T-C

Variant names:

• chr9-81880693-T-C
• rs11139451

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 0.215 in 151,936 control chromosomes in the GnomAD database, including 3,616 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 0.21 (3616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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: 0.215 AC: 32581 AN: 151818 Hom.: 3611 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.215 AC: 32602 AN: 151936 Hom.: 3616 Cov.: 32 AF XY: 0.212 AC XY: 15777 AN XY: 74268

African (AFR) AF: 0.191 AC: 7932 AN: 41438

American (AMR) AF: 0.255 AC: 3889 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3464

East Asian (EAS) AF: 0.161 AC: 832 AN: 5156

South Asian (SAS) AF: 0.144 AC: 697 AN: 4830

European-Finnish (FIN) AF: 0.217 AC: 2280 AN: 10530

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15202 AN: 67954

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.214 Hom.: 2955

Bravo AF: 0.220

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.88
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11139451; hg19: chr9-84495608;