rs1956817

Positions:

• chr14-26838608-T-C

Variant summary

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

The ENST00000550024.1(ENSG00000258081):​n.75+1806T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 152,208 control chromosomes in the GnomAD database, including 59 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 0.022 (59 hom., cov: 32)
• Consequence: ENSG00000258081 ENST00000550024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

ENSG00000258081 (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 (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903296	XR_007064092.1	n.539-142A>G		intron_variant
LOC124903296	XR_007064093.1	n.529-142A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258081	ENST00000550024.1	n.75+1806T>C		intron_variant		3
ENSG00000258081	ENST00000656336.1	n.480+113814T>C		intron_variant
ENSG00000286479	ENST00000659271.1	n.405-142A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3269 AN: 152090 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0216 AC: 3281 AN: 152208 Hom.: 59 Cov.: 32 AF XY: 0.0202 AC XY: 1506 AN XY: 74436

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.0136

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0163 Hom.: 4

Bravo AF: 0.0236

Asia WGS AF: 0.0130 AC: 45 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956817; hg19: chr14-27307814;