chr14-98083046-T-C

Position:

• chr14-98083046-T-C

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-2521A>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 0.517 in 151,590 control chromosomes in the GnomAD database, including 20,306 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 0.52 (20306 hom., cov: 30)
• Consequence: ENST00000555776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370655	XR_001750876.2	n.96-2521A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000555776.1	n.122-2521A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000663808.1	n.205-2521A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78268 AN: 151470 Hom.: 20268 Cov.: 30

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.517 AC: 78362 AN: 151590 Hom.: 20306 Cov.: 30 AF XY: 0.517 AC XY: 38258 AN XY: 74032

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.543

Alfa AF: 0.500 Hom.: 32311

Bravo AF: 0.529

Asia WGS AF: 0.483 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10782490; hg19: chr14-98549383;