rs4741756

Positions:

• chr9-2668187-A-C
• chr9-2668187-A-T

Variant summary

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

The XR_929436.3(LOC105375957):​n.26275T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,114 control chromosomes in the GnomAD database, including 5,849 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 0.28 (5849 hom., cov: 33)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

LOC105375957 (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 = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375957	XR_929436.3	n.26275T>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42106 AN: 151994 Hom.: 5839 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.277 AC: 42149 AN: 152114 Hom.: 5849 Cov.: 33 AF XY: 0.280 AC XY: 20784 AN XY: 74354

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.263

Alfa AF: 0.263 Hom.: 5442

Bravo AF: 0.276

Asia WGS AF: 0.287 AC: 998 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	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4741756; hg19: chr9-2668187;