14-56756010-T-C

Variant names:

• chr14-56756010-T-C
• rs198225
• ENST00000773249.1:n.405-30023A>G

Variant summary

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

The ENST00000773249.1(ENSG00000259133):​n.405-30023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.983 in 152,346 control chromosomes in the GnomAD database, including 73,581 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 0.98 (73581 hom., cov: 33)
• Consequence: ENSG00000259133 ENST00000773249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 0 publications found

Genes affected

ENSG00000259133 (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 (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773249.1. 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
	ENSG00000259133	ENST00000773249.1		n.405-30023A>G		intron	N/A
	ENSG00000259133	ENST00000773250.1		n.257-30023A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.983 AC: 149607 AN: 152228 Hom.: 73524 Cov.: 33

Gnomad AFR AF: 0.969

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.983 AC: 149723 AN: 152346 Hom.: 73581 Cov.: 33 AF XY: 0.983 AC XY: 73217 AN XY: 74488

African (AFR) AF: 0.969 AC: 40284 AN: 41576

American (AMR) AF: 0.991 AC: 15169 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3452 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5185 AN: 5186

South Asian (SAS) AF: 0.982 AC: 4743 AN: 4830

European-Finnish (FIN) AF: 0.987 AC: 10482 AN: 10622

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67115 AN: 68036

Other (OTH) AF: 0.987 AC: 2089 AN: 2116

Alfa AF: 0.982 Hom.: 10247

Bravo AF: 0.982

Asia WGS AF: 0.994 AC: 3457 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	1.2
DANN	Benign	0.52
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs198225; hg19: chr14-57222728;