1-147507700-C-T

Variant names:

• chr1-147507700-C-T
• rs631288
• ENST00000619867.4:n.700+6638G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000619867.4(LINC00624):​n.700+6638G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 134,336 control chromosomes in the GnomAD database, including 66 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 0.035 (66 hom., cov: 31)
• Consequence: LINC00624 ENST00000619867.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 7 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0346 (4654/134336) while in subpopulation NFE AF = 0.0428 (2538/59232). AF 95% confidence interval is 0.0415. There are 66 homozygotes in GnomAd4. There are 2247 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 66 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00624	NR_038423.2	n.700+6638G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00624	ENST00000619867.4	n.700+6638G>A		intron_variant	Intron 3 of 5	1
LINC00624	ENST00000621316.2	n.704+6638G>A		intron_variant	Intron 3 of 3	1
LINC00624	ENST00000803855.1	n.753G>A		non_coding_transcript_exon_variant	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 4652 AN: 134236 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.00137

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0598

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.0233

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0346 AC: 4654 AN: 134336 Hom.: 66 Cov.: 31 AF XY: 0.0343 AC XY: 2247 AN XY: 65514

African (AFR) AF: 0.0269 AC: 1047 AN: 38884

American (AMR) AF: 0.0308 AC: 371 AN: 12038

Ashkenazi Jewish (ASJ) AF: 0.0598 AC: 192 AN: 3210

East Asian (EAS) AF: 0.00328 AC: 16 AN: 4878

South Asian (SAS) AF: 0.0306 AC: 126 AN: 4112

European-Finnish (FIN) AF: 0.0307 AC: 283 AN: 9220

Middle Eastern (MID) AF: 0.0210 AC: 5 AN: 238

European-Non Finnish (NFE) AF: 0.0428 AC: 2538 AN: 59232

Other (OTH) AF: 0.0418 AC: 75 AN: 1794

Alfa AF: 0.0299 Hom.: 52

Bravo AF: 0.0301

Asia WGS AF: 0.0270 AC: 88 AN: 3234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.61
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs631288; hg19: chr1-146979516;