rs632737

chr6-168707998-T-A

Variant summary

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

The XR_943296.3(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_943296.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

LOC105378143 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378143	XR_943296.3	n.2143T>A		non_coding_transcript_exon_variant	1/3
LOC105378143	XR_001744472.2	n.2143T>A		non_coding_transcript_exon_variant	1/4
LOC105378143	XR_007059887.1	n.2143T>A		non_coding_transcript_exon_variant	1/4

Ensembl

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

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

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.945

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632737; hg19: -;