7-11354067-A-G

Variant names:

• chr7-11354067-A-G
• rs1076224
• ENST00000421121.5:n.114-25220A>G

Variant summary

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

The ENST00000421121.5(ENSG00000230333):​n.114-25220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,004 control chromosomes in the GnomAD database, including 17,956 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 0.46 (17956 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000421121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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	ENST00000421121.5	n.114-25220A>G		intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5	n.139-25220A>G		intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5	n.498-25220A>G		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69996 AN: 151886 Hom.: 17914 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.461 AC: 70102 AN: 152004 Hom.: 17956 Cov.: 32 AF XY: 0.453 AC XY: 33639 AN XY: 74266

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.439

Alfa AF: 0.401 Hom.: 12394

Bravo AF: 0.476

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1076224; hg19: chr7-11393694;