rs631208

Variant names:

• chr16-9305867-A-G
• rs631208
• ENST00000784364.1:n.90+18615A>G

Variant summary

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

The ENST00000784364.1(LINC02177):​n.90+18615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,938 control chromosomes in the GnomAD database, including 12,905 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 0.41 (12905 hom., cov: 31)
• Consequence: LINC02177 ENST00000784364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 9 publications found

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02177	ENST00000784364.1	n.90+18615A>G		intron_variant	Intron 1 of 2
LINC02177	ENST00000784365.1	n.85+18615A>G		intron_variant	Intron 1 of 3
LINC02177	ENST00000784366.1	n.69+18615A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61849 AN: 151820 Hom.: 12893 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.407 AC: 61891 AN: 151938 Hom.: 12905 Cov.: 31 AF XY: 0.405 AC XY: 30093 AN XY: 74256

African (AFR) AF: 0.452 AC: 18734 AN: 41432

American (AMR) AF: 0.363 AC: 5548 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1436 AN: 5154

South Asian (SAS) AF: 0.375 AC: 1800 AN: 4806

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10550

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27726 AN: 67944

Other (OTH) AF: 0.405 AC: 854 AN: 2110

Alfa AF: 0.403 Hom.: 58313

Bravo AF: 0.405

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.29
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs631208; hg19: chr16-9399724;