7-150819934-C-G

Variant names:

• chr7-150819934-C-G
• rs2110001
• XR_928171.3:n.4507G>C

Variant summary

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

The XR_928171.3(LOC105375567):​n.4507G>C 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 0.412 in 151,946 control chromosomes in the GnomAD database, including 14,110 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 0.41 (14110 hom., cov: 32)
• Consequence: LOC105375567 XR_928171.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 32 publications found

Genes affected

LOC105375567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.412 AC: 62546 AN: 151828 Hom.: 14095 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.412 AC: 62596 AN: 151946 Hom.: 14110 Cov.: 32 AF XY: 0.421 AC XY: 31221 AN XY: 74228

African (AFR) AF: 0.497 AC: 20608 AN: 41442

American (AMR) AF: 0.487 AC: 7442 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4297 AN: 5176

South Asian (SAS) AF: 0.575 AC: 2768 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3933 AN: 10514

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21028 AN: 67952

Other (OTH) AF: 0.387 AC: 816 AN: 2106

Alfa AF: 0.203 Hom.: 445

Bravo AF: 0.425

Asia WGS AF: 0.669 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2110001; hg19: chr7-150517022;