chr6-24112309-A-G

Variant names:

• chr6-24112309-A-G
• rs1419229
• ENST00000810475.1:n.94-8129A>G

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-8129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,076 control chromosomes in the GnomAD database, including 17,828 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 0.47 (17828 hom., cov: 32)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919
• Publications: 4 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810475.1. 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
	ENSG00000305332	ENST00000810475.1		n.94-8129A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71766 AN: 151958 Hom.: 17831 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.472 AC: 71785 AN: 152076 Hom.: 17828 Cov.: 32 AF XY: 0.481 AC XY: 35752 AN XY: 74326

African (AFR) AF: 0.337 AC: 13971 AN: 41486

American (AMR) AF: 0.499 AC: 7624 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1875 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5172

South Asian (SAS) AF: 0.488 AC: 2349 AN: 4818

European-Finnish (FIN) AF: 0.672 AC: 7106 AN: 10572

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35453 AN: 67964

Other (OTH) AF: 0.496 AC: 1046 AN: 2108

Alfa AF: 0.497 Hom.: 56397

Bravo AF: 0.451

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.14
DANN	Benign	0.58
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1419229;

hg19: chr6-24112537;