chr14-64905495-T-C

Variant names:

• chr14-64905495-T-C
• rs1951488
• ENST00000797561.1:n.141-3326A>G

Variant summary

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

The ENST00000797561.1(ENSG00000303859):​n.141-3326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,104 control chromosomes in the GnomAD database, including 30,464 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 0.58 (30464 hom., cov: 32)
• Consequence: ENSG00000303859 ENST00000797561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 9 publications found

Genes affected

ENSG00000303859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 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
ENSG00000303859	ENST00000797561.1	n.141-3326A>G		intron_variant	Intron 1 of 3
ENSG00000303859	ENST00000797562.1	n.100-3302A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88840 AN: 151988 Hom.: 30471 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.584 AC: 88841 AN: 152104 Hom.: 30464 Cov.: 32 AF XY: 0.581 AC XY: 43222 AN XY: 74354

African (AFR) AF: 0.219 AC: 9107 AN: 41492

American (AMR) AF: 0.694 AC: 10602 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1881 AN: 5164

South Asian (SAS) AF: 0.651 AC: 3139 AN: 4822

European-Finnish (FIN) AF: 0.669 AC: 7080 AN: 10578

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52613 AN: 67984

Other (OTH) AF: 0.621 AC: 1315 AN: 2116

Alfa AF: 0.719 Hom.: 20762

Bravo AF: 0.564

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1951488; hg19: chr14-65372213;