9-106313530-G-A

Variant names:

• chr9-106313530-G-A
• rs10978456
• XR_007061716.1:n.1248G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061716.1(LOC124902240):​n.1248G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 152,114 control chromosomes in the GnomAD database, including 184 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 0.029 (184 hom., cov: 32)
• Consequence: LOC124902240 XR_007061716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 1 publications found

Genes affected

LOC124902240 (HGNC:):

LINC01505 (HGNC:51186): (long intergenic non-protein coding RNA 1505)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435485.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01505	ENST00000435485.5	TSL:5	n.171+34340G>A		intron	N/A
	LINC01505	ENST00000637185.1	TSL:5	n.560-244942G>A		intron	N/A
	LINC01505	ENST00000793805.1		n.385-4661G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4380 AN: 151996 Hom.: 181 Cov.: 32

Gnomad AFR AF: 0.00664

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0761

Gnomad FIN AF: 0.00992

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0288 AC: 4382 AN: 152114 Hom.: 184 Cov.: 32 AF XY: 0.0297 AC XY: 2209 AN XY: 74350

African (AFR) AF: 0.00662 AC: 275 AN: 41544

American (AMR) AF: 0.0282 AC: 430 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1154 AN: 5128

South Asian (SAS) AF: 0.0761 AC: 367 AN: 4820

European-Finnish (FIN) AF: 0.00992 AC: 105 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1734 AN: 67988

Other (OTH) AF: 0.0332 AC: 70 AN: 2110

Alfa AF: 0.0311 Hom.: 277

Bravo AF: 0.0304

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.63
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs10978456; hg19: chr9-109075811;