rs9891949

Variant names:

• chr17-8195865-G-A
• rs9891949
• ENST00000761630.1:n.104+3348C>T

Variant summary

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

The ENST00000761630.1(ENSG00000299214):​n.104+3348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,970 control chromosomes in the GnomAD database, including 31,196 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 0.64 (31196 hom., cov: 33)
• Consequence: ENSG00000299214 ENST00000761630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 15 publications found

Genes affected

ENSG00000299214 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903913	XR_007065604.1	n.1016+3348C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299214	ENST00000761630.1	n.104+3348C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96793 AN: 151850 Hom.: 31175 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.637 AC: 96862 AN: 151970 Hom.: 31196 Cov.: 33 AF XY: 0.644 AC XY: 47843 AN XY: 74300

African (AFR) AF: 0.579 AC: 23975 AN: 41422

American (AMR) AF: 0.659 AC: 10057 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2530 AN: 5122

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4824

European-Finnish (FIN) AF: 0.751 AC: 7952 AN: 10584

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44941 AN: 67978

Other (OTH) AF: 0.634 AC: 1337 AN: 2108

Alfa AF: 0.654 Hom.: 5704

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.89
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs9891949; hg19: chr17-8099183;