rs405761

Variant names:

• chr9-86470211-G-A
• rs405761
• ENST00000438582.2:n.385-18176G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-86470211-G-A
• chr9-86470211-G-T

Variant summary

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

The ENST00000438582.2(ENSG00000235819):​n.385-18176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,994 control chromosomes in the GnomAD database, including 20,381 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 0.50 (20381 hom., cov: 31)
• Consequence: ENSG00000235819 ENST00000438582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 4 publications found

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724080	XR_007061636.1	n.730+55641G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235819	ENST00000438582.2	n.385-18176G>A		intron_variant	Intron 3 of 3	5
ENSG00000235819	ENST00000657061.1	n.359-18176G>A		intron_variant	Intron 1 of 1
ENSG00000235819	ENST00000739666.1	n.279-43242G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75759 AN: 151876 Hom.: 20375 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.499 AC: 75793 AN: 151994 Hom.: 20381 Cov.: 31 AF XY: 0.512 AC XY: 38015 AN XY: 74292

African (AFR) AF: 0.332 AC: 13754 AN: 41452

American (AMR) AF: 0.626 AC: 9542 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3468

East Asian (EAS) AF: 0.904 AC: 4688 AN: 5186

South Asian (SAS) AF: 0.772 AC: 3723 AN: 4824

European-Finnish (FIN) AF: 0.581 AC: 6116 AN: 10534

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34335 AN: 67958

Other (OTH) AF: 0.520 AC: 1099 AN: 2114

Alfa AF: 0.523 Hom.: 10807

Bravo AF: 0.492

Asia WGS AF: 0.803 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.68
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs405761; hg19: chr9-89085126;