rs10988428

Positions:

• chr9-129576791-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443993.1(ENSG00000227619):​n.190+1193G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,254 control chromosomes in the GnomAD database, including 1,013 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 0.093 (1013 hom., cov: 33)
• Consequence: ENST00000443993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376292	XR_930390.2	n.192+1193G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658787.1	n.415+1193G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14070 AN: 152136 Hom.: 1011 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0926 AC: 14093 AN: 152254 Hom.: 1013 Cov.: 33 AF XY: 0.0911 AC XY: 6778 AN XY: 74440

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0519

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0464

Gnomad4 FIN AF: 0.0614

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0770 Hom.: 92

Bravo AF: 0.0971

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10988428; hg19: chr9-132339070;