rs9461684

Variant names:

• chr6-31285667-C-T
• rs9461684
• ENST00000755297.1:n.32+14561C>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+14561C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,182 control chromosomes in the GnomAD database, including 1,810 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 0.14 (1810 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 35 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+14561C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22033 AN: 152064 Hom.: 1807 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.145 AC: 22063 AN: 152182 Hom.: 1810 Cov.: 32 AF XY: 0.147 AC XY: 10955 AN XY: 74414

African (AFR) AF: 0.203 AC: 8422 AN: 41490

American (AMR) AF: 0.175 AC: 2670 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3470

East Asian (EAS) AF: 0.0462 AC: 240 AN: 5194

South Asian (SAS) AF: 0.118 AC: 568 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1935 AN: 10590

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6991 AN: 68000

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.117 Hom.: 4277

Bravo AF: 0.146

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs9461684; hg19: chr6-31253444;