9-108125716-C-G

Position:

• chr9-108125716-C-G

Variant summary

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

The XR_007061722.1(LOC105376214):​n.721-72422G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,968 control chromosomes in the GnomAD database, including 29,485 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 0.62 (29485 hom., cov: 31)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376214	XR_007061722.1	n.721-72422G>C		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-72422G>C		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-72422G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93562 AN: 151850 Hom.: 29465 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.616 AC: 93631 AN: 151968 Hom.: 29485 Cov.: 31 AF XY: 0.626 AC XY: 46484 AN XY: 74282

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.629

Alfa AF: 0.624 Hom.: 3760

Bravo AF: 0.609

Asia WGS AF: 0.861 AC: 2990 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	0.55
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662694; hg19: chr9-110887996; COSMIC: COSV60389973;