rs12540248

Variant names:

• chr7-11186086-A-T
• rs12540248
• ENST00000599917.5:n.106-2453A>T

Variant summary

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

The ENST00000599917.5(ENSG00000230333):​n.106-2453A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,620 control chromosomes in the GnomAD database, including 9,205 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 0.31 (9205 hom., cov: 31)
• Consequence: ENSG00000230333 ENST00000599917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 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
ENSG00000230333	ENST00000599917.5	n.106-2453A>T		intron_variant	Intron 1 of 5	5
ENSG00000230333	ENST00000625468.2	n.349-535A>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46650 AN: 151502 Hom.: 9160 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.308 AC: 46759 AN: 151620 Hom.: 9205 Cov.: 31 AF XY: 0.303 AC XY: 22424 AN XY: 74092

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.297

Alfa AF: 0.276 Hom.: 884

Bravo AF: 0.327

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.75
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12540248; hg19: chr7-11225713;