chr4-165729864-G-A

Variant names:

• chr4-165729864-G-A
• rs10517865
• ENST00000507838.1:n.369-3231G>A

Variant summary

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

The ENST00000507838.1(LINC01179):​n.369-3231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,046 control chromosomes in the GnomAD database, including 1,079 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 0.11 (1079 hom., cov: 32)
• Consequence: LINC01179 ENST00000507838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 2 publications found

Genes affected

LINC01179 (HGNC:49556): (long intergenic non-protein coding RNA 1179)

ENSG00000287424 (HGNC:):

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 = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01179	NR_121676.1	n.369-3231G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01179	ENST00000507838.1	n.369-3231G>A		intron_variant	Intron 3 of 5	1
ENSG00000287424	ENST00000657783.2	n.5951C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287424	ENST00000668379.1	n.105+27699C>T		intron_variant	Intron 1 of 2
ENSG00000287424	ENST00000727691.1	n.106-22677C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15975 AN: 151928 Hom.: 1079 Cov.: 32

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.105 AC: 15976 AN: 152046 Hom.: 1079 Cov.: 32 AF XY: 0.105 AC XY: 7789 AN XY: 74318

African (AFR) AF: 0.0261 AC: 1083 AN: 41500

American (AMR) AF: 0.112 AC: 1704 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3466

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5180

South Asian (SAS) AF: 0.130 AC: 624 AN: 4800

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9909 AN: 67946

Other (OTH) AF: 0.116 AC: 246 AN: 2114

Alfa AF: 0.130 Hom.: 468

Bravo AF: 0.0975

Asia WGS AF: 0.0800 AC: 278 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	1.9
DANN	Benign	0.40
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10517865; hg19: chr4-166651016;