chr9-78398910-T-C

Position:

• chr9-78398910-T-C

Variant summary

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

The XR_001746759.2(LOC107987083):​n.1049-23184T>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 0.0904 in 152,066 control chromosomes in the GnomAD database, including 691 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 0.090 (691 hom., cov: 32)
• Consequence: LOC107987083 XR_001746759.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

LOC107987083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987083	XR_001746759.2	n.1049-23184T>C		intron_variant, non_coding_transcript_variant
LOC107987083	XR_001746760.2	n.1049-23184T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0904 AC: 13739 AN: 151948 Hom.: 690 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0904 AC: 13751 AN: 152066 Hom.: 691 Cov.: 32 AF XY: 0.0926 AC XY: 6879 AN XY: 74320

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0700

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.0983

Alfa AF: 0.0747 Hom.: 264

Bravo AF: 0.0958

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10867192; hg19: chr9-81013826;