rs4606154

Positions:

• chr9-13468277-G-A
• chr9-13468277-G-T

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.112+21684G>A 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 0.369 in 151,888 control chromosomes in the GnomAD database, including 10,501 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 (10501 hom., cov: 32)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375977	XR_929484.3	n.490-18826G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664438.1	n.112+21684G>A		intron_variant, non_coding_transcript_variant
LINC01235	ENST00000668698.1	n.159+19690C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56032 AN: 151770 Hom.: 10498 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.369 AC: 56066 AN: 151888 Hom.: 10501 Cov.: 32 AF XY: 0.370 AC XY: 27470 AN XY: 74208

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.392

Alfa AF: 0.369 Hom.: 5289

Bravo AF: 0.370

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4606154; hg19: chr9-13468276;