rs7146388

Variant names:

• chr14-43621725-A-G
• rs7146388
• ENST00000807481.1:n.400+29486T>C

Variant summary

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

The ENST00000807481.1(ENSG00000304974):​n.400+29486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,094 control chromosomes in the GnomAD database, including 4,418 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 0.24 (4418 hom., cov: 32)
• Consequence: ENSG00000304974 ENST00000807481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 1 publications found

Genes affected

ENSG00000304974 (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 (SAS) allele frequency at 95% confidence interval = 0.278 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
ENSG00000304974	ENST00000807481.1	n.400+29486T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36127 AN: 151976 Hom.: 4420 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.238 AC: 36144 AN: 152094 Hom.: 4418 Cov.: 32 AF XY: 0.237 AC XY: 17644 AN XY: 74372

African (AFR) AF: 0.184 AC: 7625 AN: 41508

American (AMR) AF: 0.222 AC: 3391 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1247 AN: 5176

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4822

European-Finnish (FIN) AF: 0.266 AC: 2805 AN: 10550

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18482 AN: 67966

Other (OTH) AF: 0.223 AC: 471 AN: 2114

Alfa AF: 0.252 Hom.: 799

Bravo AF: 0.233

Asia WGS AF: 0.244 AC: 842 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.39
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs7146388; hg19: chr14-44090928;