rs9386485

Variant names:

• chr6-105881180-C-T
• rs9386485
• ENST00000642235.1:n.144+3846G>A

Variant summary

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

The ENST00000642235.1(ENSG00000284999):​n.144+3846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,970 control chromosomes in the GnomAD database, including 19,366 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 (19366 hom., cov: 32)
• Consequence: ENSG00000284999 ENST00000642235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 6 publications found

Genes affected

ENSG00000284999 (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 (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642235.1. 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
	ENSG00000284999	ENST00000642235.1		n.144+3846G>A		intron	N/A
	ENSG00000284999	ENST00000644129.1		n.144+3846G>A		intron	N/A
	ENSG00000284999	ENST00000744159.1		n.237+3846G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76147 AN: 151850 Hom.: 19331 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.502 AC: 76234 AN: 151970 Hom.: 19366 Cov.: 32 AF XY: 0.501 AC XY: 37230 AN XY: 74242

African (AFR) AF: 0.578 AC: 23950 AN: 41450

American (AMR) AF: 0.432 AC: 6600 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2430 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2053 AN: 4804

European-Finnish (FIN) AF: 0.510 AC: 5366 AN: 10518

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32354 AN: 67962

Other (OTH) AF: 0.479 AC: 1012 AN: 2112

Alfa AF: 0.476 Hom.: 24977

Bravo AF: 0.497

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.13

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: rs9386485;

hg19: chr6-106329055;