chr14-46378223-A-C

Variant names:

• chr14-46378223-A-C
• rs8009432
• ENST00000555246.5:n.299+59362A>C

Variant summary

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

The ENST00000555246.5(LINC00871):​n.299+59362A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,992 control chromosomes in the GnomAD database, including 24,724 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 0.56 (24724 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 5 publications found

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555246.5. 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
	LINC00871	NR_102701.1		n.233-59958A>C		intron	N/A
	LINC00871	NR_102702.1		n.233-123084A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	ENST00000555246.5	TSL:5	n.299+59362A>C		intron	N/A
	LINC00871	ENST00000556886.1	TSL:3	n.233-59958A>C		intron	N/A
	LINC00871	ENST00000656720.1		n.234-123084A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84675 AN: 151872 Hom.: 24707 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.557 AC: 84726 AN: 151992 Hom.: 24724 Cov.: 32 AF XY: 0.564 AC XY: 41892 AN XY: 74298

African (AFR) AF: 0.421 AC: 17432 AN: 41438

American (AMR) AF: 0.709 AC: 10805 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3466

East Asian (EAS) AF: 0.970 AC: 5013 AN: 5166

South Asian (SAS) AF: 0.665 AC: 3203 AN: 4820

European-Finnish (FIN) AF: 0.542 AC: 5735 AN: 10576

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38527 AN: 67958

Other (OTH) AF: 0.586 AC: 1241 AN: 2116

Alfa AF: 0.567 Hom.: 7668

Bravo AF: 0.566

Asia WGS AF: 0.796 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.43
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs8009432; hg19: chr14-46847426;