rs9491640

Variant names:

• chr6-98471388-C-A
• rs9491640
• ENST00000848457.1:n.204+11630G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-98471388-C-A
• chr6-98471388-C-G

Variant summary

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

The ENST00000848457.1(ENSG00000310228):​n.204+11630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 151,960 control chromosomes in the GnomAD database, including 230 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 0.049 (230 hom., cov: 32)
• Consequence: ENSG00000310228 ENST00000848457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 publications found

Genes affected

ENSG00000310228 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848457.1. 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
	ENSG00000310228	ENST00000848457.1		n.204+11630G>T		intron	N/A
	ENSG00000310228	ENST00000848458.1		n.294+6163G>T		intron	N/A
	ENSG00000310228	ENST00000848459.1		n.175+11630G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7470 AN: 151842 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0743

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00775

Gnomad SAS AF: 0.00831

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0492 AC: 7481 AN: 151960 Hom.: 230 Cov.: 32 AF XY: 0.0509 AC XY: 3776 AN XY: 74230

African (AFR) AF: 0.0744 AC: 3083 AN: 41452

American (AMR) AF: 0.0624 AC: 951 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3464

East Asian (EAS) AF: 0.00757 AC: 39 AN: 5152

South Asian (SAS) AF: 0.00811 AC: 39 AN: 4808

European-Finnish (FIN) AF: 0.0637 AC: 674 AN: 10578

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0370 AC: 2517 AN: 67952

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.0383 Hom.: 423

Bravo AF: 0.0506

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9491640; hg19: chr6-98919264;