9-95663813-G-C

Variant names:

• chr9-95663813-G-C
• rs10512246
• ENST00000422343.2:n.148+13572G>C

Variant summary

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

The ENST00000422343.2(ENSG00000228142):​n.148+13572G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0422 in 152,264 control chromosomes in the GnomAD database, including 352 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 0.042 (352 hom., cov: 32)
• Consequence: ENSG00000228142 ENST00000422343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 0 publications found

Genes affected

ENSG00000228142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 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
ENSG00000228142	ENST00000422343.2	n.148+13572G>C		intron_variant	Intron 1 of 1	5
ENSG00000228142	ENST00000580326.3	n.143+13572G>C		intron_variant	Intron 1 of 2	3
ENSG00000228142	ENST00000821223.1	n.143+13572G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6406 AN: 152146 Hom.: 353 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00797

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0422 AC: 6425 AN: 152264 Hom.: 352 Cov.: 32 AF XY: 0.0419 AC XY: 3118 AN XY: 74452

African (AFR) AF: 0.124 AC: 5147 AN: 41534

American (AMR) AF: 0.0200 AC: 306 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5180

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4816

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10620

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00797 AC: 542 AN: 68028

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.00300 Hom.: 1

Bravo AF: 0.0466

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.47
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs10512246; hg19: chr9-98426095;