8-9931072-A-G

Variant names:

• chr8-9931072-A-G
• rs614197
• ENST00000843628.1:n.98-11150A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000843628.1(ENSG00000309740):​n.98-11150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,992 control chromosomes in the GnomAD database, including 10,703 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 0.33 (10703 hom., cov: 31)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 2 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000309740	ENST00000843628.1	n.98-11150A>G		intron_variant	Intron 1 of 2
ENSG00000309740	ENST00000843630.1	n.170-11150A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50110 AN: 151874 Hom.: 10673 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.330 AC: 50193 AN: 151992 Hom.: 10703 Cov.: 31 AF XY: 0.328 AC XY: 24321 AN XY: 74254

African (AFR) AF: 0.615 AC: 25482 AN: 41422

American (AMR) AF: 0.222 AC: 3393 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3464

East Asian (EAS) AF: 0.270 AC: 1398 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2860 AN: 10570

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14620 AN: 67954

Other (OTH) AF: 0.266 AC: 561 AN: 2110

Alfa AF: 0.206 Hom.: 1918

Bravo AF: 0.339

Asia WGS AF: 0.261 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	19
DANN	Benign	0.80
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs614197; hg19: chr8-9788582;