rs6604568

Variant names:

• chr1-217920809-G-A
• rs6604568
• ENST00000848869.1:n.904+834C>T

Variant summary

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

The ENST00000848869.1(ENSG00000286775):​n.904+834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,040 control chromosomes in the GnomAD database, including 37,794 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 0.70 (37793 hom., cov: 31)
  • Exomes 𝑓: 0.43 (1 hom.)
• Consequence: ENSG00000286775 ENST00000848869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 5 publications found

Genes affected

ENSG00000286775 (HGNC:):

LINC00210 (HGNC:37458): (long intergenic non-protein coding RNA 210)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372922	XR_001738466.2	n.857+741C>T		intron_variant	Intron 7 of 7
LINC00210	NR_048550.1	n.*5G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286775	ENST00000848869.1	n.904+834C>T		intron_variant	Intron 7 of 8
LINC00210	ENST00000431637.2	n.*5G>A		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106483 AN: 151910 Hom.: 37760 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.684

GnomAD4 exome AF: 0.429 AC: 6 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.429 AC XY: 6 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.429 AC: 6 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.701 AC: 106561 AN: 152026 Hom.: 37793 Cov.: 31 AF XY: 0.695 AC XY: 51662 AN XY: 74298

African (AFR) AF: 0.736 AC: 30517 AN: 41460

American (AMR) AF: 0.722 AC: 11038 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2213 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2203 AN: 5150

South Asian (SAS) AF: 0.517 AC: 2489 AN: 4812

European-Finnish (FIN) AF: 0.714 AC: 7542 AN: 10560

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48372 AN: 67980

Other (OTH) AF: 0.677 AC: 1428 AN: 2108

Alfa AF: 0.705 Hom.: 121991

Bravo AF: 0.705

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6604568; hg19: chr1-218094151;