4-171620441-T-C

Variant names:

• chr4-171620441-T-C
• rs6811723
• ENST00000508977.1:n.277+55A>G

Variant summary

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

The ENST00000508977.1(LINC02174):​n.277+55A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,236 control chromosomes in the GnomAD database, including 56,511 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 0.86 (56510 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC02174 ENST00000508977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 3 publications found

Genes affected

LINC02174 (HGNC:53037): (long intergenic non-protein coding RNA 2174)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02174	NR_147157.1		n.277+55A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02174	ENST00000508977.1	TSL:3	n.277+55A>G		intron	N/A
	LINC02174	ENST00000651666.1		n.93+15544A>G		intron	N/A
	LINC02174	ENST00000787998.1		n.172+18219A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130324 AN: 152116 Hom.: 56455 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.860

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

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) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.857 AC: 130437 AN: 152234 Hom.: 56510 Cov.: 32 AF XY: 0.852 AC XY: 63375 AN XY: 74418

African (AFR) AF: 0.913 AC: 37931 AN: 41554

American (AMR) AF: 0.793 AC: 12122 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3080 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2288 AN: 5162

South Asian (SAS) AF: 0.747 AC: 3604 AN: 4824

European-Finnish (FIN) AF: 0.887 AC: 9405 AN: 10606

Middle Eastern (MID) AF: 0.890 AC: 260 AN: 292

European-Non Finnish (NFE) AF: 0.868 AC: 59065 AN: 68012

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.880 Hom.: 7635

Bravo AF: 0.850

Asia WGS AF: 0.653 AC: 2269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6811723; hg19: chr4-172541592;