3-72091381-G-A

Position:

• chr3-72091381-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000468646.6(LINC00877):​n.366+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 ENST00000468646.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

Genes affected

LINC00877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00877	NR_104116.1	n.394+8523C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00877	ENST00000464271.1	n.390+8523C>T		intron_variant		4
LINC00877	ENST00000468646.6	n.366+8523C>T		intron_variant		2
LINC00877	ENST00000469218.6	n.255+8523C>T		intron_variant		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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.116

Alfa AF: 0.146 Hom.: 1097

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6771316; hg19: chr3-72140532;