14-74959547-G-A

Variant names:

• chr14-74959547-G-A
• rs11850328
• ENST00000748874.1:n.799+4121G>A

Variant summary

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

The ENST00000748874.1(ENSG00000297555):​n.799+4121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,024 control chromosomes in the GnomAD database, including 10,630 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 0.36 (10630 hom., cov: 32)
• Consequence: ENSG00000297555 ENST00000748874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 18 publications found

Genes affected

ENSG00000297555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748874.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297555	ENST00000748874.1		n.799+4121G>A		intron	N/A
	ENSG00000297555	ENST00000748875.1		n.403+4121G>A		intron	N/A
	ENSG00000297555	ENST00000748876.1		n.411+4121G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54439 AN: 151906 Hom.: 10624 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.358 AC: 54467 AN: 152024 Hom.: 10630 Cov.: 32 AF XY: 0.365 AC XY: 27093 AN XY: 74294

African (AFR) AF: 0.218 AC: 9057 AN: 41480

American (AMR) AF: 0.353 AC: 5390 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5168

South Asian (SAS) AF: 0.393 AC: 1891 AN: 4814

European-Finnish (FIN) AF: 0.540 AC: 5704 AN: 10566

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28517 AN: 67942

Other (OTH) AF: 0.385 AC: 809 AN: 2104

Alfa AF: 0.390 Hom.: 40703

Bravo AF: 0.335

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs11850328; hg19: chr14-75426250;