14-65103668-C-A

Variant names:

• chr14-65103668-C-A
• rs1953232
• ENST00000845055.1:n.461+404C>A

Variant summary

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

The ENST00000845055.1(ENSG00000309897):​n.461+404C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,038 control chromosomes in the GnomAD database, including 20,577 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 0.48 (20577 hom., cov: 32)
• Consequence: ENSG00000309897 ENST00000845055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 10 publications found

Genes affected

ENSG00000309897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845055.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309897	ENST00000845055.1		n.461+404C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73609 AN: 151920 Hom.: 20540 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.485 AC: 73696 AN: 152038 Hom.: 20577 Cov.: 32 AF XY: 0.482 AC XY: 35839 AN XY: 74298

African (AFR) AF: 0.780 AC: 32367 AN: 41470

American (AMR) AF: 0.309 AC: 4721 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2146 AN: 5166

South Asian (SAS) AF: 0.492 AC: 2371 AN: 4818

European-Finnish (FIN) AF: 0.421 AC: 4441 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25345 AN: 67972

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.375 Hom.: 6308

Bravo AF: 0.485

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1953232;

hg19: chr14-65570386;