9-1456797-C-T

Position:

• chr9-1456797-C-T

Variant summary

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

The XR_002956872.2(LOC102723803):​n.357-7346C>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 0.367 in 151,796 control chromosomes in the GnomAD database, including 10,506 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 0.37 (10506 hom., cov: 32)
• Consequence: LOC102723803 XR_002956872.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

LOC102723803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723803	XR_002956872.2	n.357-7346C>T		intron_variant, non_coding_transcript_variant
LOC102723803	XR_929415.3	n.357-7346C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55779 AN: 151678 Hom.: 10510 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.367 AC: 55785 AN: 151796 Hom.: 10506 Cov.: 32 AF XY: 0.360 AC XY: 26702 AN XY: 74154

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.385

Alfa AF: 0.302 Hom.: 1164

Bravo AF: 0.367

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412259; hg19: chr9-1456797;