rs7227159

Positions:

• chr18-71533616-C-T

Variant summary

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

The NR_038326.1(LINC01541):​n.331+598G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,066 control chromosomes in the GnomAD database, including 3,209 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 0.20 (3209 hom., cov: 32)
• Consequence: LINC01541 NR_038326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

LINC01541 (HGNC:51309): (long intergenic non-protein coding RNA 1541)

LOC107985179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01541	NR_038326.1	n.331+598G>A		intron_variant, non_coding_transcript_variant
LOC107985179	XR_001753502.1	n.65-14355C>T		intron_variant, non_coding_transcript_variant
LINC01541	NR_038325.1	n.331+598G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01541	ENST00000568095.5	n.331+598G>A		intron_variant, non_coding_transcript_variant		1
LINC01541	ENST00000566582.1	n.312+598G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30500 AN: 150948 Hom.: 3201 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.202 AC: 30555 AN: 151066 Hom.: 3209 Cov.: 32 AF XY: 0.200 AC XY: 14738 AN XY: 73776

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.202

Alfa AF: 0.192 Hom.: 1521

Bravo AF: 0.206

Asia WGS AF: 0.159 AC: 551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7227159; hg19: chr18-69200852;