rs17104630

Positions:

• chr14-36530844-A-G

Variant summary

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

The ENST00000634305.1(ENSG00000283098):​n.322+82007A>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 0.0809 in 152,282 control chromosomes in the GnomAD database, including 633 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 0.081 (633 hom., cov: 33)
• Consequence: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

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 (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370453	XR_001750715.2	n.520+5636A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634305.1	n.322+82007A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12312 AN: 152164 Hom.: 629 Cov.: 33

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0809 AC: 12323 AN: 152282 Hom.: 633 Cov.: 33 AF XY: 0.0838 AC XY: 6243 AN XY: 74472

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.0809

Alfa AF: 0.0856 Hom.: 737

Bravo AF: 0.0813

Asia WGS AF: 0.130 AC: 449 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	0.36
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17104630; hg19: chr14-37000049;