rs2215921

Variant names:

• chr16-9603476-G-A
• rs2215921
• ENST00000634367.3:n.623-11045G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-9603476-G-A
• chr16-9603476-G-C

Variant summary

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

The ENST00000784503.1(LINC02177):​n.652+36886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,016 control chromosomes in the GnomAD database, including 9,086 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 0.33 (9086 hom., cov: 32)
• Consequence: LINC02177 ENST00000784503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784503.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02177	ENST00000634367.3	TSL:5	n.623-11045G>A		intron	N/A
	LINC02177	ENST00000784503.1		n.652+36886G>A		intron	N/A
	LINC02177	ENST00000784504.1		n.480+36886G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49822 AN: 151898 Hom.: 9092 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.328 AC: 49824 AN: 152016 Hom.: 9086 Cov.: 32 AF XY: 0.326 AC XY: 24231 AN XY: 74298

African (AFR) AF: 0.176 AC: 7298 AN: 41466

American (AMR) AF: 0.302 AC: 4605 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2801 AN: 5168

South Asian (SAS) AF: 0.299 AC: 1443 AN: 4822

European-Finnish (FIN) AF: 0.375 AC: 3956 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27408 AN: 67976

Other (OTH) AF: 0.351 AC: 743 AN: 2114

Alfa AF: 0.378 Hom.: 48110

Bravo AF: 0.318

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.85
PhyloP100		1.0

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: rs2215921;

hg19: chr16-9697333;