9-19472462-A-C

Position:

• chr9-19472462-A-C

Variant summary

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

The XR_007061431.1(LOC105375988):​n.399+1962A>C 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 0.319 in 151,964 control chromosomes in the GnomAD database, including 8,224 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 0.32 (8224 hom., cov: 32)
• Consequence: LOC105375988 XR_007061431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

LOC105375988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375988	XR_007061431.1	n.399+1962A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48424 AN: 151846 Hom.: 8205 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.319 AC: 48488 AN: 151964 Hom.: 8224 Cov.: 32 AF XY: 0.327 AC XY: 24313 AN XY: 74248

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.268

Alfa AF: 0.262 Hom.: 5531

Bravo AF: 0.317

Asia WGS AF: 0.438 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11792752; hg19: chr9-19472460;