rs7130929

Variant names:

• chr11-18046616-C-A
• rs7130929
• ENST00000787024.1:n.97-18432C>A

Variant summary

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

The ENST00000787024.1(ENSG00000302464):​n.97-18432C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,902 control chromosomes in the GnomAD database, including 12,396 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 0.40 (12396 hom., cov: 31)
• Consequence: ENSG00000302464 ENST00000787024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 9 publications found

Genes affected

ENSG00000302464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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
ENSG00000302464	ENST00000787024.1	n.97-18432C>A		intron_variant	Intron 1 of 1
ENSG00000302464	ENST00000787025.1	n.98-15322C>A		intron_variant	Intron 1 of 2
ENSG00000302464	ENST00000787026.1	n.94-15322C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60706 AN: 151784 Hom.: 12386 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.400 AC: 60762 AN: 151902 Hom.: 12396 Cov.: 31 AF XY: 0.394 AC XY: 29249 AN XY: 74226

African (AFR) AF: 0.424 AC: 17546 AN: 41402

American (AMR) AF: 0.347 AC: 5294 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3462

East Asian (EAS) AF: 0.224 AC: 1158 AN: 5166

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4060 AN: 10530

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28554 AN: 67930

Other (OTH) AF: 0.415 AC: 877 AN: 2112

Alfa AF: 0.410 Hom.: 21524

Bravo AF: 0.399

Asia WGS AF: 0.301 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		-0.28
PromoterAI		-0.0016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7130929; hg19: chr11-18068163;