10-121007334-C-G

Variant names:

• chr10-121007334-C-G
• rs3981055
• XR_001747611.2:n.351-7772G>C

Variant summary

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

The XR_001747611.2(LOC105378521):​n.351-7772G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,104 control chromosomes in the GnomAD database, including 13,788 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 (13788 hom., cov: 33)
• Consequence: LOC105378521 XR_001747611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 0 publications found

Genes affected

LOC105378521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.409 AC: 62226 AN: 151986 Hom.: 13778 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.409 AC: 62254 AN: 152104 Hom.: 13788 Cov.: 33 AF XY: 0.419 AC XY: 31187 AN XY: 74350

African (AFR) AF: 0.274 AC: 11382 AN: 41502

American (AMR) AF: 0.521 AC: 7955 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3470

East Asian (EAS) AF: 0.744 AC: 3854 AN: 5180

South Asian (SAS) AF: 0.607 AC: 2929 AN: 4826

European-Finnish (FIN) AF: 0.475 AC: 5014 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28629 AN: 67980

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.274 Hom.: 692

Bravo AF: 0.410

Asia WGS AF: 0.645 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.82
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3981055;

hg19: chr10-122766847;