rs9323985

Positions:

• chr14-98083318-T-C

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-2793A>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 0.0717 in 152,160 control chromosomes in the GnomAD database, including 737 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 0.072 (737 hom., cov: 32)
• Consequence: ENST00000555776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370655	XR_001750876.2	n.96-2793A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555776.1	n.122-2793A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000663808.1	n.205-2793A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0715 AC: 10878 AN: 152042 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0717 AC: 10905 AN: 152160 Hom.: 737 Cov.: 32 AF XY: 0.0742 AC XY: 5521 AN XY: 74398

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0604 Hom.: 51

Bravo AF: 0.0854

Asia WGS AF: 0.132 AC: 458 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
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: rs9323985; hg19: chr14-98549655;