rs9490860

chr6-123668596-A-Cchr6-123668596-A-Gchr6-123668596-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650190.1(ENSG00000285941):n.572-264A>C variant causes a intron, non coding transcript 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: ENST00000650190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377981	XR_942943.3	n.287-264A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650190.1	n.572-264A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.298

Alfa AF: 0.267 Hom.: 5706

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

Splicing

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

Publications

LitVar

Other links and lift over

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