rs1075830

Variant names:

• chr14-92309818-A-C
• rs1075830
• ENST00000826664.1:n.258+5274A>C

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.258+5274A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,968 control chromosomes in the GnomAD database, including 15,483 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 0.43 (15483 hom., cov: 31)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 4 publications found

Genes affected

ENSG00000307514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307514	ENST00000826664.1		n.258+5274A>C		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.253+5274A>C		intron	N/A
	ENSG00000307514	ENST00000826667.1		n.311+5274A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64894 AN: 151850 Hom.: 15477 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.427 AC: 64918 AN: 151968 Hom.: 15483 Cov.: 31 AF XY: 0.424 AC XY: 31497 AN XY: 74286

African (AFR) AF: 0.228 AC: 9441 AN: 41456

American (AMR) AF: 0.370 AC: 5650 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1462 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1887 AN: 5144

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5699 AN: 10564

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37361 AN: 67930

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.461 Hom.: 5775

Bravo AF: 0.400

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.50
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1075830; hg19: chr14-92776162;