1-221302557-A-G

Variant names:

• chr1-221302557-A-G
• rs75849835
• ENST00000779986.1:n.547-3807T>C

Variant summary

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

The ENST00000779986.1(LINC02817):​n.547-3807T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0211 in 152,336 control chromosomes in the GnomAD database, including 59 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 0.021 (59 hom., cov: 32)
• Consequence: LINC02817 ENST00000779986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 2 publications found

Genes affected

LINC02817 (HGNC:32042): (long intergenic non-protein coding RNA 2817)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0211 (3218/152336) while in subpopulation SAS AF = 0.0381 (184/4830). AF 95% confidence interval is 0.0336. There are 59 homozygotes in GnomAd4. There are 1596 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 59 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779986.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02817	ENST00000779986.1		n.547-3807T>C		intron	N/A
	LINC02817	ENST00000779987.1		n.75-62T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3217 AN: 152218 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.00536

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0211 AC: 3218 AN: 152336 Hom.: 59 Cov.: 32 AF XY: 0.0214 AC XY: 1596 AN XY: 74482

African (AFR) AF: 0.00534 AC: 222 AN: 41578

American (AMR) AF: 0.0182 AC: 278 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4830

European-Finnish (FIN) AF: 0.0229 AC: 243 AN: 10616

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1901 AN: 68032

Other (OTH) AF: 0.0213 AC: 45 AN: 2116

Alfa AF: 0.0215 Hom.: 7

Bravo AF: 0.0201

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs75849835; hg19: chr1-221475899;