chr1-147517855-G-C

Variant names:

• chr1-147517855-G-C
• rs681814
• ENST00000619867.4:n.21C>G

Variant summary

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

The ENST00000619867.4(LINC00624):​n.21C>G 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 0.992 in 152,386 control chromosomes in the GnomAD database, including 74,909 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 0.99 (74885 hom., cov: 32)
  • Exomes 𝑓: 1.0 (24 hom.)
• Consequence: LINC00624 ENST00000619867.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 publications found

Genes affected

LINC00624 (HGNC:44254): (long intergenic non-protein coding RNA 624)

ENSG00000304519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.21C>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.21C>G		non_coding_transcript_exon_variant	Exon 1 of 6	1
LINC00624	ENST00000621316.2	n.25C>G		non_coding_transcript_exon_variant	Exon 1 of 4	1
LINC00624	ENST00000803843.1	n.25C>G		non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.992 AC: 150933 AN: 152220 Hom.: 74827 Cov.: 32

Gnomad AFR AF: 0.988

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.998

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.990

GnomAD4 exome AF: 1.00 AC: 48 AN: 48 Hom.: 24 Cov.: 0 AF XY: 1.00 AC XY: 34 AN XY: 34

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 40 AN: 40

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.992 AC: 151050 AN: 152338 Hom.: 74885 Cov.: 32 AF XY: 0.992 AC XY: 73886 AN XY: 74494

African (AFR) AF: 0.988 AC: 41081 AN: 41574

American (AMR) AF: 0.993 AC: 15209 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3408 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.999 AC: 4813 AN: 4820

European-Finnish (FIN) AF: 0.998 AC: 10596 AN: 10622

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67465 AN: 68042

Other (OTH) AF: 0.991 AC: 2096 AN: 2116

Alfa AF: 0.990 Hom.: 3443

Bravo AF: 0.991

Asia WGS AF: 0.999 AC: 3473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.20
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs681814; hg19: chr1-146989679;