rs1402405

Variant names:

• chr6-24090269-G-A
• rs1402405
• ENST00000810475.1:n.94-30169G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-24090269-G-A
• chr6-24090269-G-T

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-30169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,018 control chromosomes in the GnomAD database, including 22,805 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 0.55 (22805 hom., cov: 32)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 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.94-30169G>A		intron	N/A
	ENSG00000305347	ENST00000810528.1		n.140-10253C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82931 AN: 151900 Hom.: 22790 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.546 AC: 82974 AN: 152018 Hom.: 22805 Cov.: 32 AF XY: 0.544 AC XY: 40405 AN XY: 74326

African (AFR) AF: 0.558 AC: 23114 AN: 41456

American (AMR) AF: 0.521 AC: 7953 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1916 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2713 AN: 5162

South Asian (SAS) AF: 0.645 AC: 3109 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4943 AN: 10564

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37374 AN: 67962

Other (OTH) AF: 0.570 AC: 1202 AN: 2110

Alfa AF: 0.549 Hom.: 97984

Bravo AF: 0.546

Asia WGS AF: 0.574 AC: 1994 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.22
PhyloP100		-0.83

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: rs1402405;

hg19: chr6-24090497;