rs9912203

Variant names:

• chr17-43367777-G-A
• rs9912203
• ENST00000658096.1:n.695+9894C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000658096.1(LINC00910):​n.695+9894C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 24 publications found

Genes affected

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

LOC124904147 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658096.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00910	ENST00000658096.1		n.695+9894C>T		intron	N/A
	LINC00910	ENST00000661340.1		n.708+9894C>T		intron	N/A
	LINC00910	ENST00000662750.1		n.708+9894C>T		intron	N/A

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

African (AFR) AF: 0.593 AC: 24580 AN: 41434

American (AMR) AF: 0.370 AC: 5639 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1909 AN: 5166

South Asian (SAS) AF: 0.523 AC: 2522 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4330 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23025 AN: 67954

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.360 Hom.: 48354

Bravo AF: 0.425

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.33
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9912203; hg19: chr17-41445145;