rs1412256

chr9-1464067-C-Gchr9-1464067-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.357-76C>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 0.143 in 151,980 control chromosomes in the GnomAD database, including 2,875 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 0.14 (2875 hom., cov: 32)
• Consequence: LOC102723803 XR_002956872.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

Genes affected

LOC102723803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723803	XR_002956872.2	n.357-76C>G		intron_variant, non_coding_transcript_variant
LOC102723803	XR_929415.3	n.357-76C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21629 AN: 151862 Hom.: 2865 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.143 AC: 21674 AN: 151980 Hom.: 2875 Cov.: 32 AF XY: 0.137 AC XY: 10197 AN XY: 74262

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0798

Gnomad4 SAS AF: 0.0868

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0594

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0390 Hom.: 53

Bravo AF: 0.155

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412256; hg19: chr9-1464067;