rs5768939

Variant names:

• chr22-46138166-A-G
• rs5768939
• XR_007068140.1:n.3783T>C

Variant summary

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

The XR_007068140.1(LOC124905138):​n.3783T>C 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 0.117 in 152,274 control chromosomes in the GnomAD database, including 1,304 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 0.12 (1304 hom., cov: 33)
• Consequence: LOC124905138 XR_007068140.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 6 publications found

Genes affected

LOC124905138 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905138	XR_007068140.1	n.3783T>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124905137	XR_007068138.1	n.*99A>G		downstream_gene_variant
LOC124905137	XR_007068139.1	n.*99A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310037	ENST00000846710.1	n.558+2750T>C		intron_variant	Intron 2 of 2
ENSG00000310037	ENST00000846711.1	n.541+2750T>C		intron_variant	Intron 2 of 2
ENSG00000310052	ENST00000846781.1	n.607+371A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17865 AN: 152156 Hom.: 1303 Cov.: 33

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.117 AC: 17864 AN: 152274 Hom.: 1304 Cov.: 33 AF XY: 0.117 AC XY: 8746 AN XY: 74454

African (AFR) AF: 0.0297 AC: 1236 AN: 41576

American (AMR) AF: 0.133 AC: 2031 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.119 AC: 615 AN: 5188

South Asian (SAS) AF: 0.157 AC: 757 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1560 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10958 AN: 68008

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.135 Hom.: 1678

Bravo AF: 0.112

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs5768939; hg19: chr22-46534046;