7-33063100-G-C

Variant names:

• chr7-33063100-G-C
• rs10262141
• XR_007060277.1:n.-85G>C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901610 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901610	XR_007060277.1	n.-85G>C		upstream_gene_variant
LOC124901610	XR_007060278.1	n.-85G>C		upstream_gene_variant
LOC124901610	XR_007060279.1	n.-85G>C		upstream_gene_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.659

Alfa AF: 0.619 Hom.: 1829

Bravo AF: 0.686

Asia WGS AF: 0.543 AC: 1892 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10262141; hg19: chr7-33102712;