XR_001744300.1:n.60-33515G>A

Variant names:

• chr6-112803099-C-T
• rs6934970
• XR_001744300.1:n.60-33515G>A

Variant summary

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

The XR_001744300.1(LOC107986634):​n.60-33515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,748 control chromosomes in the GnomAD database, including 51,268 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 0.82 (51268 hom., cov: 31)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 6 publications found

Genes affected

LOC107986634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986634	XR_001744300.1	n.60-33515G>A		intron_variant	Intron 1 of 6
LOC107986634	XR_001744301.2	n.59+43663G>A		intron_variant	Intron 1 of 5
LOC107986634	XR_001744302.1	n.60-33515G>A		intron_variant	Intron 1 of 6
LOC107986634	XR_001744303.1	n.60-33515G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123711 AN: 151630 Hom.: 51253 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.816 AC: 123765 AN: 151748 Hom.: 51268 Cov.: 31 AF XY: 0.817 AC XY: 60619 AN XY: 74188

African (AFR) AF: 0.645 AC: 26722 AN: 41430

American (AMR) AF: 0.879 AC: 13389 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4633 AN: 5164

South Asian (SAS) AF: 0.917 AC: 4427 AN: 4830

European-Finnish (FIN) AF: 0.875 AC: 9255 AN: 10572

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59699 AN: 67746

Other (OTH) AF: 0.823 AC: 1732 AN: 2104

Alfa AF: 0.847 Hom.: 18664

Bravo AF: 0.806

Asia WGS AF: 0.902 AC: 3135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6934970; hg19: chr6-113124301;