rs6771316

Variant names:

• chr3-72091381-G-A
• rs6771316
• ENST00000464271.1:n.390+8523C>T

Variant summary

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

The ENST00000464271.1(LINC00877):​n.390+8523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,250 control chromosomes in the GnomAD database, including 1,311 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 0.13 (1311 hom., cov: 33)
• Consequence: LINC00877 ENST00000464271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 11 publications found

Genes affected

LINC00877 (HGNC:27706): (long intergenic non-protein coding RNA 877)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00877	NR_104116.1	n.394+8523C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00877	ENST00000464271.1	n.390+8523C>T		intron_variant	Intron 2 of 2	4
LINC00877	ENST00000468646.6	n.366+8523C>T		intron_variant	Intron 2 of 6	2
LINC00877	ENST00000469218.6	n.255+8523C>T		intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19566 AN: 152132 Hom.: 1314 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.128 AC: 19564 AN: 152250 Hom.: 1311 Cov.: 33 AF XY: 0.122 AC XY: 9104 AN XY: 74446

African (AFR) AF: 0.113 AC: 4691 AN: 41542

American (AMR) AF: 0.0772 AC: 1181 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3470

East Asian (EAS) AF: 0.114 AC: 593 AN: 5182

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4824

European-Finnish (FIN) AF: 0.0987 AC: 1047 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10878 AN: 68006

Other (OTH) AF: 0.116 AC: 246 AN: 2116

Alfa AF: 0.149 Hom.: 3792

Bravo AF: 0.125

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6771316; hg19: chr3-72140532;