rs4871297

Variant names:

• chr8-122693916-G-A
• rs4871297
• ENST00000521608.2:n.175C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-122693916-G-A
• chr8-122693916-G-C
• chr8-122693916-G-T

Variant summary

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

The ENST00000521608.2(LINC01151):​n.175C>T 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 0.546 in 152,144 control chromosomes in the GnomAD database, including 22,816 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 0.55 (22816 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC01151 ENST00000521608.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 11 publications found

Genes affected

LINC01151 (HGNC:49471): (long intergenic non-protein coding RNA 1151)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521608.2. 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
	LINC01151	NR_126348.1		n.191C>T		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01151	ENST00000521608.2	TSL:4	n.175C>T		non_coding_transcript_exon	Exon 1 of 4
	LINC01151	ENST00000656927.1		n.195C>T		non_coding_transcript_exon	Exon 1 of 4
	LINC01151	ENST00000659897.1		n.231C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82963 AN: 152022 Hom.: 22800 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.546 AC: 83006 AN: 152140 Hom.: 22816 Cov.: 33 AF XY: 0.543 AC XY: 40400 AN XY: 74390

African (AFR) AF: 0.587 AC: 24368 AN: 41494

American (AMR) AF: 0.444 AC: 6791 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3472

East Asian (EAS) AF: 0.636 AC: 3287 AN: 5168

South Asian (SAS) AF: 0.576 AC: 2777 AN: 4824

European-Finnish (FIN) AF: 0.521 AC: 5507 AN: 10580

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36615 AN: 67988

Other (OTH) AF: 0.527 AC: 1115 AN: 2116

Alfa AF: 0.541 Hom.: 47079

Bravo AF: 0.535

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.5
DANN	Benign	0.82
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4871297; hg19: chr8-123706155;