XR_007060277.1:n.-85G>C

Variant names:

• chr7-33063100-G-C
• rs10262141
• ENST00000788221.1:n.192G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_007060277.1(LOC124901610):​n.-85G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,168 control chromosomes in the GnomAD database, including 36,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.69 (36363 hom., cov: 33)
• Consequence: LOC124901610 XR_007060277.1 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.710
• Publications: 4 publications found

Genes affected

ENSG00000302625 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 7-33063100-G-C is Benign according to our data. Variant chr7-33063100-G-C is described in ClinVar as Benign. ClinVar VariationId is 1225236.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788221.1. 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
	ENSG00000302625	ENST00000788221.1		n.192G>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000302625	ENST00000788220.1		n.124+98G>C		intron	N/A
	ENSG00000302625	ENST00000788224.1		n.124+98G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104708 AN: 152050 Hom.: 36323 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.689 AC: 104803 AN: 152168 Hom.: 36363 Cov.: 33 AF XY: 0.690 AC XY: 51299 AN XY: 74370

African (AFR) AF: 0.689 AC: 28618 AN: 41526

American (AMR) AF: 0.719 AC: 10989 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1942 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2541 AN: 5160

South Asian (SAS) AF: 0.604 AC: 2919 AN: 4832

European-Finnish (FIN) AF: 0.759 AC: 8034 AN: 10590

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47729 AN: 67996

Other (OTH) AF: 0.659 AC: 1392 AN: 2112

Alfa AF: 0.619 Hom.: 1829

Bravo AF: 0.686

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.42
PhyloP100		-0.71
PromoterAI		-0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10262141; hg19: chr7-33102712;