rs135561

Variant names:

• chr22-46143764-G-A
• rs135561
• ENST00000846781.1:n.908G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-46143764-G-A
• chr22-46143764-G-C
• chr22-46143764-G-T

Variant summary

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

The ENST00000846781.1(ENSG00000310052):​n.908G>A 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 0.366 in 152,114 control chromosomes in the GnomAD database, including 12,300 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 0.37 (12300 hom., cov: 33)
• Consequence: ENSG00000310052 ENST00000846781.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 6 publications found

Genes affected

ENSG00000310052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=14.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905138	XR_007068140.1	n.465C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310052	ENST00000846781.1	n.908G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000310052	ENST00000846782.1	n.872G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000310052	ENST00000846783.1	n.710G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55578 AN: 151996 Hom.: 12272 Cov.: 33

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.366 AC: 55657 AN: 152114 Hom.: 12300 Cov.: 33 AF XY: 0.356 AC XY: 26483 AN XY: 74380

African (AFR) AF: 0.617 AC: 25607 AN: 41472

American (AMR) AF: 0.236 AC: 3616 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 779 AN: 3468

East Asian (EAS) AF: 0.0810 AC: 420 AN: 5188

South Asian (SAS) AF: 0.207 AC: 1000 AN: 4828

European-Finnish (FIN) AF: 0.256 AC: 2712 AN: 10576

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20356 AN: 67970

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.331 Hom.: 15969

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	14
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs135561; hg19: -;