ENST00000413406.1:n.76-10731G>A

Variant names:

• chr7-108936229-G-A
• rs848330
• ENST00000413406.1:n.76-10731G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413406.1(ENSG00000229603):​n.76-10731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,952 control chromosomes in the GnomAD database, including 2,627 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 0.14 (2627 hom., cov: 32)
• Consequence: ENSG00000229603 ENST00000413406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

ENSG00000229603 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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
ENSG00000229603	ENST00000413406.1	n.76-10731G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21251 AN: 151834 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.140 AC: 21311 AN: 151952 Hom.: 2627 Cov.: 32 AF XY: 0.137 AC XY: 10200 AN XY: 74340

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.0589

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.125

Alfa AF: 0.110 Hom.: 272

Bravo AF: 0.151

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs848330; hg19: chr7-108576286;