rs9262570

Variant names:

• chr6-31044708-C-T
• rs9262570
• ENST00000745182.1:n.90-1078C>T

Variant summary

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

The ENST00000745182.1(ENSG00000297077):​n.90-1078C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0252 in 152,262 control chromosomes in the GnomAD database, including 63 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 0.025 (63 hom., cov: 32)
• Consequence: ENSG00000297077 ENST00000745182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 8 publications found

Genes affected

ENSG00000297077 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745182.1. 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
	ENSG00000297077	ENST00000745182.1		n.90-1078C>T		intron	N/A
	ENSG00000297077	ENST00000745183.1		n.178-1078C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3838 AN: 152144 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0252 AC: 3843 AN: 152262 Hom.: 63 Cov.: 32 AF XY: 0.0255 AC XY: 1899 AN XY: 74448

African (AFR) AF: 0.0316 AC: 1314 AN: 41538

American (AMR) AF: 0.0231 AC: 354 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3466

East Asian (EAS) AF: 0.0656 AC: 340 AN: 5182

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4824

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0216 AC: 1469 AN: 68026

Other (OTH) AF: 0.0313 AC: 66 AN: 2110

Alfa AF: 0.0224 Hom.: 96

Bravo AF: 0.0275

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.7
DANN	Benign	0.84
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9262570; hg19: chr6-31012485;