rs1205106

Variant names:

• chr14-71802951-G-A
• rs1205106
• ENST00000787281.1:n.193-1632G>A

Variant summary

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

The ENST00000787281.1(ENSG00000302484):​n.193-1632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,892 control chromosomes in the GnomAD database, including 23,879 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 0.56 (23879 hom., cov: 31)
• Consequence: ENSG00000302484 ENST00000787281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 3 publications found

Genes affected

ENSG00000302484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302484	ENST00000787281.1	n.193-1632G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85011 AN: 151774 Hom.: 23856 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.560 AC: 85078 AN: 151892 Hom.: 23879 Cov.: 31 AF XY: 0.561 AC XY: 41673 AN XY: 74242

African (AFR) AF: 0.550 AC: 22753 AN: 41380

American (AMR) AF: 0.579 AC: 8845 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3073 AN: 5174

South Asian (SAS) AF: 0.719 AC: 3462 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5381 AN: 10516

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.545 AC: 37058 AN: 67962

Other (OTH) AF: 0.600 AC: 1265 AN: 2108

Alfa AF: 0.562 Hom.: 15007

Bravo AF: 0.562

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs1205106; hg19: chr14-72269668;