rs4562969

Variant names:

• chr14-106520947-C-A
• rs4562969
• ENST00000619530.1:n.1373C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-106520947-C-A
• chr14-106520947-C-T

Variant summary

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

The ENST00000619530.1(LINC00221):​n.1373C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,554 control chromosomes in the GnomAD database, including 28,803 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 0.61 (28803 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00221 ENST00000619530.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 4 publications found

Genes affected

LINC00221 (HGNC:20169): (long intergenic non-protein coding RNA 221)

IGH (HGNC:5477):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=4.062).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619530.1. 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
	LINC00221	ENST00000619530.1	TSL:2	n.1373C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92315 AN: 151440 Hom.: 28777 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.638

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.610 AC: 92376 AN: 151554 Hom.: 28803 Cov.: 32 AF XY: 0.602 AC XY: 44529 AN XY: 74012

African (AFR) AF: 0.502 AC: 20712 AN: 41266

American (AMR) AF: 0.636 AC: 9661 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2371 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2415 AN: 5052

South Asian (SAS) AF: 0.515 AC: 2467 AN: 4788

European-Finnish (FIN) AF: 0.600 AC: 6326 AN: 10540

Middle Eastern (MID) AF: 0.688 AC: 194 AN: 282

European-Non Finnish (NFE) AF: 0.679 AC: 46125 AN: 67938

Other (OTH) AF: 0.639 AC: 1345 AN: 2104

Alfa AF: 0.704 Hom.: 6712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.1
PhyloP100		0.17

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: rs4562969;