rs2108179

Variant names:

• chr7-41933746-G-A
• rs2108179
• XR_007060294.1:n.-156C>T

Variant summary

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

The XR_007060294.1(LOC124901618):​n.-156C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,022 control chromosomes in the GnomAD database, including 27,064 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 0.59 (27064 hom., cov: 32)
• Consequence: LOC124901618 XR_007060294.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 3 publications found

Genes affected

LOC124901618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90347 AN: 151904 Hom.: 27035 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.595 AC: 90429 AN: 152022 Hom.: 27064 Cov.: 32 AF XY: 0.595 AC XY: 44225 AN XY: 74332

African (AFR) AF: 0.633 AC: 26224 AN: 41458

American (AMR) AF: 0.566 AC: 8644 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2733 AN: 5146

South Asian (SAS) AF: 0.624 AC: 3009 AN: 4822

European-Finnish (FIN) AF: 0.657 AC: 6942 AN: 10572

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39032 AN: 67960

Other (OTH) AF: 0.597 AC: 1259 AN: 2110

Alfa AF: 0.586 Hom.: 4225

Bravo AF: 0.589

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs2108179; hg19: chr7-41973344;