9-23557229-T-G

Variant names:

• chr9-23557229-T-G
• rs10511729
• ENST00000640307.1:n.1835-2612A>C

Variant summary

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

The ENST00000640307.1(ENSG00000283982):​n.1835-2612A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,974 control chromosomes in the GnomAD database, including 10,035 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 0.35 (10035 hom., cov: 32)
• Consequence: ENSG00000283982 ENST00000640307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 7 publications found

Genes affected

ENSG00000283982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929563	NR_121602.1	n.1847-2612A>C		intron_variant	Intron 11 of 27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283982	ENST00000640307.1	n.1835-2612A>C		intron_variant	Intron 11 of 27	1
ENSG00000283982	ENST00000785123.1	n.239-16505A>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53372 AN: 151856 Hom.: 10031 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.351 AC: 53402 AN: 151974 Hom.: 10035 Cov.: 32 AF XY: 0.356 AC XY: 26412 AN XY: 74282

African (AFR) AF: 0.450 AC: 18635 AN: 41444

American (AMR) AF: 0.267 AC: 4065 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3466

East Asian (EAS) AF: 0.608 AC: 3129 AN: 5148

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3829 AN: 10558

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19500 AN: 67976

Other (OTH) AF: 0.336 AC: 710 AN: 2116

Alfa AF: 0.305 Hom.: 16964

Bravo AF: 0.348

Asia WGS AF: 0.516 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10511729; hg19: chr9-23557227;