rs9490860

Variant names:

• chr6-123668596-A-C
• rs9490860
• ENST00000650190.1:n.572-264A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-123668596-A-C
• chr6-123668596-A-G
• chr6-123668596-A-T

Variant summary

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

The ENST00000650190.1(ENSG00000285941):​n.572-264A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,036 control chromosomes in the GnomAD database, including 10,160 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 0.34 (10160 hom., cov: 32)
• Consequence: ENSG00000285941 ENST00000650190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 publications found

Genes affected

ENSG00000285941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650190.1. 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
	ENSG00000285941	ENST00000650190.1		n.572-264A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51951 AN: 151918 Hom.: 10152 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.342 AC: 51994 AN: 152036 Hom.: 10160 Cov.: 32 AF XY: 0.349 AC XY: 25916 AN XY: 74310

African (AFR) AF: 0.463 AC: 19176 AN: 41448

American (AMR) AF: 0.440 AC: 6732 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3303 AN: 5156

South Asian (SAS) AF: 0.534 AC: 2570 AN: 4816

European-Finnish (FIN) AF: 0.225 AC: 2380 AN: 10560

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16327 AN: 67986

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.284 Hom.: 17754

Bravo AF: 0.363

Asia WGS AF: 0.551 AC: 1913 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.045

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: rs9490860;

hg19: chr6-123989741;

COSMIC: COSV60279096;