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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378521	XR_001747611.2	n.351-7772G>C		intron_variant	Intron 3 of 3

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs3981055; hg19: chr10-122766847;