9-87058705-C-T

Position:

• chr9-87058705-C-T

Variant summary

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

The XR_007061638.1(LOC124902196):​n.124+5295C>T 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 0.497 in 152,002 control chromosomes in the GnomAD database, including 19,532 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 0.50 (19532 hom., cov: 32)
• Consequence: LOC124902196 XR_007061638.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

LOC124902196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902196	XR_007061638.1	n.124+5295C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75511 AN: 151884 Hom.: 19525 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.497 AC: 75537 AN: 152002 Hom.: 19532 Cov.: 32 AF XY: 0.496 AC XY: 36850 AN XY: 74316

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.541

Alfa AF: 0.524 Hom.: 9604

Bravo AF: 0.503

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350564; hg19: chr9-89673620;