rs16934200

chr9-1799943-T-C

Variant summary

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

The XR_001746599.1(LOC105375951):n.142+81031T>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 0.113 in 152,258 control chromosomes in the GnomAD database, including 1,085 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 0.11 (1085 hom., cov: 32)
• Consequence: LOC105375951 XR_001746599.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

LOC105375951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375951	XR_001746599.1	n.142+81031T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17100 AN: 152140 Hom.: 1080 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0930

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.113 AC: 17133 AN: 152258 Hom.: 1085 Cov.: 32 AF XY: 0.114 AC XY: 8519 AN XY: 74464

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0763

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.101

Alfa AF: 0.111 Hom.: 1118

Bravo AF: 0.108

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16934200; hg19: chr9-1799943;