rs632737

Variant names:

• chr6-168707998-T-A
• rs632737
• XR_001744472.2:n.2143T>A

Variant summary

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

The XR_001744472.2(LOC105378143):​n.2143T>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 0.937 in 152,310 control chromosomes in the GnomAD database, including 66,961 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 0.94 (66961 hom., cov: 32)
• Consequence: LOC105378143 XR_001744472.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 5 publications found

Genes affected

LOC105378143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378143	XR_001744472.2	n.2143T>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105378143	XR_007059887.1	n.2143T>A		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105378143	XR_943296.3	n.2143T>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289090	ENST00000746859.1	n.308+10443T>A		intron_variant	Intron 2 of 4
ENSG00000289090	ENST00000746861.1	n.282-1701T>A		intron_variant	Intron 2 of 2
ENSG00000289090	ENST00000746862.1	n.279-479T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142615 AN: 152192 Hom.: 66909 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.937 AC: 142727 AN: 152310 Hom.: 66961 Cov.: 32 AF XY: 0.936 AC XY: 69738 AN XY: 74470

African (AFR) AF: 0.984 AC: 40917 AN: 41578

American (AMR) AF: 0.917 AC: 14019 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4979 AN: 5182

South Asian (SAS) AF: 0.952 AC: 4590 AN: 4822

European-Finnish (FIN) AF: 0.921 AC: 9765 AN: 10608

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62136 AN: 68032

Other (OTH) AF: 0.945 AC: 2000 AN: 2116

Alfa AF: 0.927 Hom.: 8108

Bravo AF: 0.940

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.80
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs632737; hg19: -;