rs7853368

chr9-13457921-G-C

Variant summary

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

The ENST00000664438.1(ENSG00000226197):n.112+11328G>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 0.5 in 151,990 control chromosomes in the GnomAD database, including 20,969 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 (20969 hom., cov: 32)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

Genes affected

(HGNC:):

LINC01235 (HGNC:49769): (long intergenic non-protein coding RNA 1235)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375977	XR_929484.3	n.489+11328G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664438.1	n.112+11328G>C		intron_variant, non_coding_transcript_variant
LINC01235	ENST00000668698.1	n.160-24972C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75919 AN: 151874 Hom.: 20969 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.500 AC: 75946 AN: 151990 Hom.: 20969 Cov.: 32 AF XY: 0.502 AC XY: 37328 AN XY: 74306

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.509

Alfa AF: 0.562 Hom.: 3125

Bravo AF: 0.473

Asia WGS AF: 0.420 AC: 1463 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	6.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7853368; hg19: chr9-13457920;