rs10491557

chr9-19497272-G-A

Variant summary

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

The XR_007061431.1(LOC105375988):n.692+9710G>A 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 0.0349 in 152,222 control chromosomes in the GnomAD database, including 194 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 0.035 (194 hom., cov: 32)
• Consequence: LOC105375988 XR_007061431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

LOC105375988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375988	XR_007061431.1	n.692+9710G>A		intron_variant, non_coding_transcript_variant
LOC105375988	XR_007061430.1	n.556+9710G>A		intron_variant, non_coding_transcript_variant
LOC105375988	XR_929510.4	n.412+9710G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5307 AN: 152104 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0258

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0349 AC: 5305 AN: 152222 Hom.: 194 Cov.: 32 AF XY: 0.0375 AC XY: 2793 AN XY: 74442

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.0258

Gnomad4 ASJ AF: 0.0829

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0238 Hom.: 6

Bravo AF: 0.0338

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.070
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491557; hg19: chr9-19497270;