rs472975

Variant names:

• chr1-185565344-A-G
• rs472975
• ENST00000608417.6:n.167-2016T>C

Variant summary

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

The ENST00000608417.6(LINC01350):​n.167-2016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,028 control chromosomes in the GnomAD database, including 15,677 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 0.44 (15677 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01350 ENST00000608417.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 3 publications found

Genes affected

LINC01350 (HGNC:50575): (long intergenic non-protein coding RNA 1350)

LOC107985239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608417.6. 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
	LINC01350	NR_110793.1		n.147-2016T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01350	ENST00000608417.6	TSL:1	n.167-2016T>C		intron	N/A
	LINC01350	ENST00000439633.7	TSL:5	n.406+130T>C		intron	N/A
	LINC01350	ENST00000609066.6	TSL:2	n.402+130T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66837 AN: 151912 Hom.: 15661 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.440 AC: 66890 AN: 152028 Hom.: 15677 Cov.: 32 AF XY: 0.442 AC XY: 32849 AN XY: 74310

African (AFR) AF: 0.584 AC: 24210 AN: 41466

American (AMR) AF: 0.323 AC: 4929 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3466

East Asian (EAS) AF: 0.152 AC: 786 AN: 5182

South Asian (SAS) AF: 0.410 AC: 1977 AN: 4824

European-Finnish (FIN) AF: 0.506 AC: 5347 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27221 AN: 67948

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.437 Hom.: 1939

Bravo AF: 0.429

Asia WGS AF: 0.331 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.29
DANN	Benign	0.83
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs472975; hg19: chr1-185534476;