XR_007066738.1:n.738A>G

Variant names:

• chr1-173492069-T-C
• rs75302560
• XR_007066738.1:n.738A>G

Variant summary

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

The XR_007066738.1(LOC124904456):​n.738A>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 0.0549 in 152,260 control chromosomes in the GnomAD database, including 410 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 0.055 (410 hom., cov: 32)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 publications found

Genes affected

LOC124904456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779396.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301502	ENST00000779396.1		n.*186A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8353 AN: 152142 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.0322

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0549 AC: 8365 AN: 152260 Hom.: 410 Cov.: 32 AF XY: 0.0565 AC XY: 4205 AN XY: 74426

African (AFR) AF: 0.0322 AC: 1338 AN: 41548

American (AMR) AF: 0.0365 AC: 559 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5170

South Asian (SAS) AF: 0.0981 AC: 473 AN: 4824

European-Finnish (FIN) AF: 0.0606 AC: 642 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3587 AN: 68028

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0564 Hom.: 476

Bravo AF: 0.0512

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.30
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs75302560; hg19: chr1-173461208;