21-33938601-A-G

Position:

• chr21-33938601-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038883.2(LINC00649):​n.621+6859A>G variant causes a intron, non coding transcript 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 NR_038883.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00649	NR_038883.2	n.621+6859A>G		intron_variant, non_coding_transcript_variant
LINC00649	NR_134558.1	n.55-7209A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00649	ENST00000596365.5	n.247-7209A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.200

Alfa AF: 0.219 Hom.: 1199

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717205; hg19: chr21-35310905;