rs16976171

Positions:

• chr18-42479656-G-T

Variant summary

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

The NR_046174.2(LINC00907):​n.872+24667G>T 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 0.0517 in 151,480 control chromosomes in the GnomAD database, including 358 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 0.052 (358 hom., cov: 32)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.872+24667G>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.652+24667G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+24667G>T		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000585639.5	n.631+24667G>T		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000589068.5	n.837+24667G>T		intron_variant, non_coding_transcript_variant		2
LINC00907	ENST00000591381.5	n.472+24667G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7825 AN: 151378 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0517 AC: 7838 AN: 151480 Hom.: 358 Cov.: 32 AF XY: 0.0527 AC XY: 3901 AN XY: 73972

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0406

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0240 Hom.: 92

Bravo AF: 0.0564

Asia WGS AF: 0.113 AC: 392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16976171; hg19: chr18-40059621;