rs7201988

Variant names:

• chr16-9514649-C-G
• rs7201988
• ENST00000652999.1:n.284C>G

Variant summary

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

The ENST00000652999.1(LINC02177):​n.284C>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,036 control chromosomes in the GnomAD database, including 8,994 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 0.34 (8992 hom., cov: 31)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: LINC02177 ENST00000652999.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 3 publications found

Genes affected

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

LOC101927026 (HGNC:):

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 = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652999.1. 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
	LOC101927026	NR_188389.1		n.665-50C>G		intron	N/A
	LOC101927026	NR_188390.1		n.665-50C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02177	ENST00000652999.1		n.284C>G		splice_region non_coding_transcript_exon	Exon 4 of 5
	LINC02177	ENST00000659345.1		n.2246C>G		non_coding_transcript_exon	Exon 1 of 2
	LINC02177	ENST00000784369.1		n.435C>G		splice_region non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51247 AN: 151846 Hom.: 8988 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.194 AC: 14 AN: 72 Hom.: 2 Cov.: 0 AF XY: 0.203 AC XY: 13 AN XY: 64

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.179 AC: 10 AN: 56

Other (OTH) AF: 0.167 AC: 2 AN: 12

GnomAD4 genome AF: 0.337 AC: 51266 AN: 151964 Hom.: 8992 Cov.: 31 AF XY: 0.339 AC XY: 25197 AN XY: 74282

African (AFR) AF: 0.416 AC: 17244 AN: 41404

American (AMR) AF: 0.393 AC: 6009 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3466

East Asian (EAS) AF: 0.361 AC: 1862 AN: 5156

South Asian (SAS) AF: 0.326 AC: 1567 AN: 4800

European-Finnish (FIN) AF: 0.275 AC: 2904 AN: 10562

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19563 AN: 67966

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.309 Hom.: 926

Bravo AF: 0.349

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.48
PhyloP100		-0.034

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7201988;

hg19: chr16-9608506;