rs12334460

Variant names:

• chr8-9122179-T-C
• rs12334460
• ENST00000733758.1:n.1071-382A>G

Variant summary

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

The ENST00000733758.1(ENSG00000295900):​n.1071-382A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,050 control chromosomes in the GnomAD database, including 10,184 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 0.36 (10184 hom., cov: 32)
• Consequence: ENSG00000295900 ENST00000733758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

Genes affected

ENSG00000295900 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268402	XR_007060803.1	n.886+3786A>G		intron_variant	Intron 2 of 2
LOC112268402	XR_007060804.1	n.887-3692A>G		intron_variant	Intron 2 of 2
LOC112268402	XR_007060805.1	n.813-382A>G		intron_variant	Intron 1 of 3
LOC112268402	XR_007060806.1	n.813-3692A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295900	ENST00000733758.1	n.1071-382A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53981 AN: 151932 Hom.: 10182 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.355 AC: 53999 AN: 152050 Hom.: 10184 Cov.: 32 AF XY: 0.345 AC XY: 25678 AN XY: 74322

African (AFR) AF: 0.453 AC: 18775 AN: 41428

American (AMR) AF: 0.260 AC: 3980 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1171 AN: 3464

East Asian (EAS) AF: 0.119 AC: 615 AN: 5180

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2720 AN: 10578

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24453 AN: 67978

Other (OTH) AF: 0.349 AC: 738 AN: 2112

Alfa AF: 0.356 Hom.: 3898

Bravo AF: 0.358

Asia WGS AF: 0.196 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12334460; hg19: chr8-8979689;