rs644695

Variant names:

• chr3-177573909-A-G
• rs644695
• ENST00000439009.1:n.147+131799A>G

Variant summary

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

The ENST00000442937.6(LINC00578):​n.289+34416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,262 control chromosomes in the GnomAD database, including 942 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 0.10 (942 hom., cov: 32)
• Consequence: LINC00578 ENST00000442937.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 8 publications found

Genes affected

LINC00578 (HGNC:43807): (long intergenic non-protein coding RNA 578)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442937.6. 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
	LINC00578	NR_047568.1		n.289+34416A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000439009.1	TSL:4	n.147+131799A>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.289+34416A>G		intron	N/A
	LINC00578	ENST00000656037.1		n.185-55508A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15455 AN: 152144 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.101 AC: 15449 AN: 152262 Hom.: 942 Cov.: 32 AF XY: 0.0997 AC XY: 7423 AN XY: 74448

African (AFR) AF: 0.0266 AC: 1107 AN: 41568

American (AMR) AF: 0.108 AC: 1660 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3470

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5170

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4826

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10612

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9991 AN: 67994

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.131 Hom.: 4485

Bravo AF: 0.0994

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.043

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs644695;

hg19: chr3-177291697;