rs11626637

Variant names:

• chr14-46253459-A-G
• rs11626637
• ENST00000555246.5:n.250+41655A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000555246.5(LINC00871):​n.250+41655A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 152,228 control chromosomes in the GnomAD database, including 440 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 0.067 (440 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.232+41655A>G		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.232+41655A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.250+41655A>G		intron_variant	Intron 3 of 5	5
LINC00871	ENST00000556886.1	n.232+41655A>G		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.233+41655A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10153 AN: 152110 Hom.: 440 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0667 AC: 10157 AN: 152228 Hom.: 440 Cov.: 32 AF XY: 0.0634 AC XY: 4722 AN XY: 74430

African (AFR) AF: 0.0183 AC: 761 AN: 41564

American (AMR) AF: 0.0569 AC: 870 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4828

European-Finnish (FIN) AF: 0.0571 AC: 606 AN: 10604

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6952 AN: 68002

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0816 Hom.: 510

Bravo AF: 0.0661

Asia WGS AF: 0.0190 AC: 68 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11626637; hg19: chr14-46722662;