rs12540248

Positions:

• chr7-11186086-A-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, non coding transcript 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: ENST00000599917.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000599917.5	n.106-2453A>T		intron_variant, non_coding_transcript_variant		5
	ENST00000625468.2	n.349-535A>T		intron_variant, non_coding_transcript_variant		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;