rs4741756

Variant names:

• chr9-2668187-A-C
• rs4741756
• XR_929436.3:n.26275T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-2668187-A-C
• chr9-2668187-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375957	XR_929436.3	n.26275T>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286670	ENST00000768783.1	n.114-126T>G		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.157-126T>G		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.157-3112T>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.283 AC: 11745 AN: 41494

American (AMR) AF: 0.262 AC: 4001 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1240 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1600 AN: 5170

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2779 AN: 10588

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18396 AN: 67962

Other (OTH) AF: 0.263 AC: 557 AN: 2114

Alfa AF: 0.267 Hom.: 8118

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4741756; hg19: chr9-2668187;