chr9-7952034-A-C

Variant names:

• chr9-7952034-A-C
• rs10491573
• ENST00000656028.1:n.477+8534T>G

Variant summary

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

The ENST00000656028.1(ENSG00000231902):​n.477+8534T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,706 control chromosomes in the GnomAD database, including 3,918 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 0.20 (3918 hom., cov: 31)
• Consequence: ENSG00000231902 ENST00000656028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 0 publications found

Genes affected

ENSG00000231902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375971	XR_929462.3	n.499+8534T>G		intron_variant	Intron 2 of 4
LOC105375971	XR_929463.3	n.499+8534T>G		intron_variant	Intron 2 of 4
LOC105375971	XR_929464.3	n.499+8534T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231902	ENST00000656028.1	n.477+8534T>G		intron_variant	Intron 2 of 5
ENSG00000231902	ENST00000668681.2	n.400+8796T>G		intron_variant	Intron 1 of 3
ENSG00000231902	ENST00000813700.1	n.400+8796T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30374 AN: 151588 Hom.: 3923 Cov.: 31

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.200 AC: 30368 AN: 151706 Hom.: 3918 Cov.: 31 AF XY: 0.204 AC XY: 15150 AN XY: 74114

African (AFR) AF: 0.0455 AC: 1887 AN: 41444

American (AMR) AF: 0.306 AC: 4647 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2336 AN: 5092

South Asian (SAS) AF: 0.346 AC: 1661 AN: 4802

European-Finnish (FIN) AF: 0.172 AC: 1812 AN: 10536

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16202 AN: 67864

Other (OTH) AF: 0.221 AC: 465 AN: 2106

Alfa AF: 0.206 Hom.: 472

Bravo AF: 0.203

Asia WGS AF: 0.342 AC: 1186 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.53
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10491573; hg19: chr9-7952034;