7-155217003-T-G

Variant summary

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

The XR_007060603.1(LOC124901783):n.5528T>G 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 0.158 in 151,934 control chromosomes in the GnomAD database, including 2,248 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 0.16 (2248 hom., cov: 32)
• Consequence: LOC124901783 XR_007060603.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

LOC124901783 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901783	XR_007060603.1	n.5528T>G		non_coding_transcript_exon_variant	2/2
LOC124901784	XR_007060604.1	n.340A>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663395.1	n.1314T>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24001 AN: 151816 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.158 AC: 24018 AN: 151934 Hom.: 2248 Cov.: 32 AF XY: 0.166 AC XY: 12314 AN XY: 74220

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.150

Alfa AF: 0.101 Hom.: 204

Bravo AF: 0.153

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561176; hg19: chr7-155008713;