4-10357340-G-C

Variant names:

• chr4-10357340-G-C
• rs7681212
• XR_007058031.1:n.2770C>G

Variant summary

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

The XR_007058031.1(LOC124900667):​n.2770C>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 0.818 in 152,238 control chromosomes in the GnomAD database, including 51,154 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 0.82 (51154 hom., cov: 33)
• Consequence: LOC124900667 XR_007058031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

LOC124900667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.818 AC: 124360 AN: 152120 Hom.: 51100 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.818 AC: 124467 AN: 152238 Hom.: 51154 Cov.: 33 AF XY: 0.819 AC XY: 60935 AN XY: 74436

African (AFR) AF: 0.900 AC: 37386 AN: 41558

American (AMR) AF: 0.752 AC: 11495 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5062 AN: 5188

South Asian (SAS) AF: 0.848 AC: 4094 AN: 4826

European-Finnish (FIN) AF: 0.801 AC: 8481 AN: 10588

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52868 AN: 68004

Other (OTH) AF: 0.813 AC: 1718 AN: 2112

Alfa AF: 0.800 Hom.: 5714

Bravo AF: 0.816

Asia WGS AF: 0.899 AC: 3127 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	0.023
DANN	Benign	0.34
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7681212; hg19: chr4-10358964;