chr9-112198179-T-C

Variant names:

• chr9-112198179-T-C
• rs10759532

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 0.55 in 149,036 control chromosomes in the GnomAD database, including 23,958 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 0.55 (23958 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.550 AC: 81926 AN: 148920 Hom.: 23941 Cov.: 25

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.550 AC: 81984 AN: 149036 Hom.: 23958 Cov.: 25 AF XY: 0.546 AC XY: 39599 AN XY: 72550

African (AFR) AF: 0.773 AC: 31309 AN: 40528

American (AMR) AF: 0.498 AC: 7346 AN: 14764

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1356 AN: 3446

East Asian (EAS) AF: 0.371 AC: 1866 AN: 5024

South Asian (SAS) AF: 0.496 AC: 2339 AN: 4718

European-Finnish (FIN) AF: 0.398 AC: 3992 AN: 10020

Middle Eastern (MID) AF: 0.431 AC: 124 AN: 288

European-Non Finnish (NFE) AF: 0.477 AC: 32086 AN: 67266

Other (OTH) AF: 0.502 AC: 1043 AN: 2078

Alfa AF: 0.303 Hom.: 546

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.30
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10759532; hg19: chr9-114960459;