rs1405608

Variant names:

• chr12-19834435-G-A
• rs1405608
• ENST00000535764.1:n.153+58832G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-19834435-G-A
• chr12-19834435-G-C

Variant summary

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

The ENST00000535764.1(ENSG00000255910):​n.153+58832G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,788 control chromosomes in the GnomAD database, including 39,247 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 0.72 (39247 hom., cov: 30)
• Consequence: ENSG00000255910 ENST00000535764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 5 publications found

Genes affected

ENSG00000255910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000535764.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255910	ENST00000535764.1	TSL:3	n.153+58832G>A		intron	N/A
	ENSG00000255910	ENST00000716354.1		n.256+58832G>A		intron	N/A
	ENSG00000255910	ENST00000716355.1		n.186+58832G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108740 AN: 151670 Hom.: 39230 Cov.: 30

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.717 AC: 108800 AN: 151788 Hom.: 39247 Cov.: 30 AF XY: 0.711 AC XY: 52689 AN XY: 74150

African (AFR) AF: 0.690 AC: 28557 AN: 41400

American (AMR) AF: 0.655 AC: 9988 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2859 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3826 AN: 5160

South Asian (SAS) AF: 0.688 AC: 3314 AN: 4816

European-Finnish (FIN) AF: 0.631 AC: 6586 AN: 10440

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51338 AN: 67944

Other (OTH) AF: 0.725 AC: 1532 AN: 2112

Alfa AF: 0.748 Hom.: 177294

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.4
DANN	Benign	0.61
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1405608; hg19: chr12-19987369;