chr9-136141208-T-C

Position:

• chr9-136141208-T-C

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 0.108 in 152,220 control chromosomes in the GnomAD database, including 1,822 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 0.11 (1822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.108 AC: 16374 AN: 152102 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.108 AC: 16425 AN: 152220 Hom.: 1822 Cov.: 32 AF XY: 0.104 AC XY: 7708 AN XY: 74446

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0603

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.00565

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0570 Hom.: 446

Bravo AF: 0.118

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1747856; hg19: chr9-139033054;