9-7919153-T-C

Position:

• chr9-7919153-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668681.1(ENSG00000231902):​n.567-4412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,176 control chromosomes in the GnomAD database, including 52,400 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 0.83 (52400 hom., cov: 32)
• Consequence: ENSG00000231902 ENST00000668681.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

ENSG00000231902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375971	XR_929463.3	n.671-4412A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231902	ENST00000668681.1	n.567-4412A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125703 AN: 152058 Hom.: 52350 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.827 AC: 125814 AN: 152176 Hom.: 52400 Cov.: 32 AF XY: 0.826 AC XY: 61429 AN XY: 74374

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.805

Alfa AF: 0.774 Hom.: 58623

Bravo AF: 0.835

Asia WGS AF: 0.890 AC: 3093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.74
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2208742; hg19: chr9-7919153;