chr7-108936229-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000229603 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413406.1. 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
	ENSG00000229603	ENST00000413406.1	TSL:4	n.76-10731G>A		intron	N/A

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

African (AFR) AF: 0.330 AC: 13689 AN: 41430

American (AMR) AF: 0.0867 AC: 1322 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3462

East Asian (EAS) AF: 0.143 AC: 739 AN: 5184

South Asian (SAS) AF: 0.0735 AC: 355 AN: 4828

European-Finnish (FIN) AF: 0.0474 AC: 502 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4150 AN: 67890

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.117 Hom.: 315

Bravo AF: 0.151

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.31
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs848330; hg19: chr7-108576286;