chr4-171620441-T-C

Position:

• chr4-171620441-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02174	NR_147157.1	n.277+55A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02174	ENST00000508977.1	n.277+55A>G		intron_variant		3
LINC02174	ENST00000651666.1	n.93+15544A>G		intron_variant

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

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.860

Alfa AF: 0.879 Hom.: 7314

Bravo AF: 0.850

Asia WGS AF: 0.653 AC: 2269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6811723; hg19: chr4-172541592;