rs717205

Variant names:

• chr21-33938601-A-G
• rs717205
• ENST00000427447.6:n.630+6859A>G

Variant summary

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

The ENST00000427447.6(LINC00649):​n.630+6859A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,012 control chromosomes in the GnomAD database, including 3,394 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 0.19 (3394 hom., cov: 30)
• Consequence: LINC00649 ENST00000427447.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 3 publications found

Genes affected

LINC00649 (HGNC:44305): (long intergenic non-protein coding RNA 649)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00649	NR_038883.2	n.621+6859A>G		intron_variant	Intron 1 of 2
LINC00649	NR_134558.1	n.55-7209A>G		intron_variant	Intron 1 of 2
LINC00649	NR_134559.1	n.*229A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00649	ENST00000427447.6	n.630+6859A>G		intron_variant	Intron 1 of 2	1
LINC00649	ENST00000400353.7	n.135-7209A>G		intron_variant	Intron 1 of 2	3
LINC00649	ENST00000596365.5	n.247-7209A>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28716 AN: 151894 Hom.: 3395 Cov.: 30

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.189 AC: 28717 AN: 152012 Hom.: 3394 Cov.: 30 AF XY: 0.190 AC XY: 14107 AN XY: 74298

African (AFR) AF: 0.0681 AC: 2824 AN: 41494

American (AMR) AF: 0.142 AC: 2163 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.0738 AC: 382 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3293 AN: 10528

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17434 AN: 67944

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.215 Hom.: 1508

Bravo AF: 0.169

Asia WGS AF: 0.180 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.040
DANN	Benign	0.57
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs717205; hg19: chr21-35310905;