rs1886106

chr9-108406363-G-Achr9-108406363-G-C

Variant summary

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

The XR_007061722.1(LOC105376214):n.326-30767C>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 0.254 in 151,992 control chromosomes in the GnomAD database, including 5,537 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 0.25 (5537 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.326-30767C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.326-30767C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.326-30767C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38685 AN: 151874 Hom.: 5542 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.254 AC: 38670 AN: 151992 Hom.: 5537 Cov.: 32 AF XY: 0.253 AC XY: 18830 AN XY: 74302

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.300

Alfa AF: 0.264 Hom.: 947

Bravo AF: 0.243

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886106; hg19: chr9-111168643;