9-107599719-C-G

Position:

• chr9-107599719-C-G

Variant summary

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

The XR_930217.2(LOC105376205):​n.926+6222C>G 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 0.35 in 151,968 control chromosomes in the GnomAD database, including 10,664 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 0.35 (10664 hom., cov: 32)
• Consequence: LOC105376205 XR_930217.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

Genes affected

LOC105376205 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376205	XR_930217.2	n.926+6222C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53085 AN: 151850 Hom.: 10617 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.350 AC: 53192 AN: 151968 Hom.: 10664 Cov.: 32 AF XY: 0.345 AC XY: 25609 AN XY: 74262

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.354

Alfa AF: 0.310 Hom.: 1053

Bravo AF: 0.372

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6477578; hg19: chr9-110362000;