rs9323989

Positions:

• chr14-98121332-T-C

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-40807A>G 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 0.332 in 151,994 control chromosomes in the GnomAD database, including 8,742 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 0.33 (8742 hom., cov: 32)
• Consequence: ENST00000555776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.96-40807A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555776.1	n.122-40807A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50495 AN: 151876 Hom.: 8740 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.332 AC: 50535 AN: 151994 Hom.: 8742 Cov.: 32 AF XY: 0.329 AC XY: 24473 AN XY: 74284

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.358

Alfa AF: 0.383 Hom.: 22977

Bravo AF: 0.327

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.043
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9323989; hg19: chr14-98587669;