rs1959290

Variant names:

• chr14-86672385-T-C
• rs1959290
• ENST00000778903.1:n.349-14874A>G

Variant summary

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

The ENST00000778903.1(ENSG00000301442):​n.349-14874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,066 control chromosomes in the GnomAD database, including 2,629 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 0.18 (2629 hom., cov: 32)
• Consequence: ENSG00000301442 ENST00000778903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 4 publications found

Genes affected

ENSG00000301442 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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
ENSG00000301442	ENST00000778903.1	n.349-14874A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26888 AN: 151948 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.177 AC: 26893 AN: 152066 Hom.: 2629 Cov.: 32 AF XY: 0.175 AC XY: 13022 AN XY: 74304

African (AFR) AF: 0.121 AC: 5014 AN: 41510

American (AMR) AF: 0.130 AC: 1992 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 800 AN: 3472

East Asian (EAS) AF: 0.0134 AC: 69 AN: 5160

South Asian (SAS) AF: 0.128 AC: 619 AN: 4824

European-Finnish (FIN) AF: 0.275 AC: 2908 AN: 10560

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14904 AN: 67954

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.209 Hom.: 453

Bravo AF: 0.162

Asia WGS AF: 0.0800 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1959290; hg19: chr14-87138729;