rs1359076

Variant names:

• chr9-108283554-C-T
• rs1359076
• XR_001746881.2:n.720+27112G>A

Variant summary

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

The XR_001746881.2(LOC105376214):​n.720+27112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,156 control chromosomes in the GnomAD database, including 2,775 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 0.12 (2775 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 2 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.720+27112G>A		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.720+27112G>A		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.720+27112G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17620 AN: 152038 Hom.: 2771 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.116 AC: 17644 AN: 152156 Hom.: 2775 Cov.: 32 AF XY: 0.112 AC XY: 8364 AN XY: 74400

African (AFR) AF: 0.357 AC: 14791 AN: 41466

American (AMR) AF: 0.0578 AC: 884 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5170

South Asian (SAS) AF: 0.0364 AC: 176 AN: 4830

European-Finnish (FIN) AF: 0.00594 AC: 63 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1126 AN: 68002

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0648 Hom.: 1953

Bravo AF: 0.128

Asia WGS AF: 0.0460 AC: 159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1359076; hg19: chr9-111045834;