9-78681003-T-C

Position:

• chr9-78681003-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 0.721 in 151,958 control chromosomes in the GnomAD database, including 39,913 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 0.72 (39913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109416 AN: 151838 Hom.: 39869 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.721 AC: 109520 AN: 151958 Hom.: 39913 Cov.: 31 AF XY: 0.722 AC XY: 53652 AN XY: 74272

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.733

Alfa AF: 0.705 Hom.: 7101

Bravo AF: 0.732

Asia WGS AF: 0.651 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722642; hg19: chr9-81295919;