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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377981	XR_942943.3	n.287-264A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285941	ENST00000650190.1	n.572-264A>C		intron_variant	Intron 5 of 9

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 v4.3

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

Other links and lift over

dbSNP: rs9490860; hg19: chr6-123989741; COSMIC: COSV60279096;