rs6845080

Variant names:

• chr4-82613701-T-C
• rs6845080
• ENST00000426551.5:n.638+171A>G

Variant summary

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

The ENST00000426551.5(LINC00575):​n.638+171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,066 control chromosomes in the GnomAD database, including 7,431 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 0.31 (7431 hom., cov: 32)
• Consequence: LINC00575 ENST00000426551.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 3 publications found

Genes affected

LINC00575 (HGNC:21342): (long intergenic non-protein coding RNA 575)

ENSG00000286490 (HGNC:):

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 = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426551.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00575	NR_024087.1		n.638+171A>G		intron	N/A
	LINC00575	NR_024088.1		n.576+171A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00575	ENST00000426551.5	TSL:1	n.638+171A>G		intron	N/A
	LINC00575	ENST00000515811.1	TSL:1	n.576+171A>G		intron	N/A
	LINC00575	ENST00000651054.1		n.749+171A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46951 AN: 151946 Hom.: 7426 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.309 AC: 46983 AN: 152066 Hom.: 7431 Cov.: 32 AF XY: 0.313 AC XY: 23248 AN XY: 74312

African (AFR) AF: 0.321 AC: 13323 AN: 41450

American (AMR) AF: 0.253 AC: 3866 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1968 AN: 5180

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4812

European-Finnish (FIN) AF: 0.388 AC: 4095 AN: 10558

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20384 AN: 67992

Other (OTH) AF: 0.304 AC: 643 AN: 2114

Alfa AF: 0.300 Hom.: 9079

Bravo AF: 0.301

Asia WGS AF: 0.304 AC: 1055 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	0.79
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6845080; hg19: chr4-83534854;