rs9359896

Positions:

• chr6-90587895-C-T

Variant summary

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

The XR_007059680.1(LOC124901363):​n.1102C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,266 control chromosomes in the GnomAD database, including 476 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 0.060 (476 hom., cov: 32)
• Consequence: LOC124901363 XR_007059680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

LOC124901363 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901363	XR_007059680.1	n.1102C>T		non_coding_transcript_exon_variant	1/2
LOC124901363	XR_007059679.1	n.548C>T		non_coding_transcript_exon_variant	2/3
LOC124901363	XR_007059681.1	n.557+148C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0594 AC: 9035 AN: 152148 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.00698

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0595 AC: 9060 AN: 152266 Hom.: 476 Cov.: 32 AF XY: 0.0584 AC XY: 4351 AN XY: 74464

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.00698

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0500 Hom.: 50

Bravo AF: 0.0668

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9359896; hg19: chr6-91297614;