rs9912203

Positions:

• chr17-43367777-G-A
• chr17-43367777-G-C

Variant summary

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

The ENST00000658096.1(LINC00910):​n.695+9894C>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 0.425 in 151,960 control chromosomes in the GnomAD database, including 14,713 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 0.42 (14713 hom., cov: 31)
• Consequence: LINC00910 ENST00000658096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LINC00910 (HGNC:44361): (long intergenic non-protein coding RNA 910)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00910	ENST00000658096.1	n.695+9894C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000661340.1	n.708+9894C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000662750.1	n.708+9894C>T		intron_variant, non_coding_transcript_variant
LINC00910	ENST00000664824.1	n.695+9894C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64431 AN: 151842 Hom.: 14669 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.425 AC: 64521 AN: 151960 Hom.: 14713 Cov.: 31 AF XY: 0.428 AC XY: 31820 AN XY: 74266

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.417

Alfa AF: 0.350 Hom.: 21979

Bravo AF: 0.425

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.33
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9912203; hg19: chr17-41445145;