rs10772967

Variant names:

• chr12-16808066-T-A
• rs10772967
• XR_931397.3:n.674-20019A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-16808066-T-A
• chr12-16808066-T-G

Variant summary

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

The XR_931397.3(LOC105369677):​n.674-20019A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,170 control chromosomes in the GnomAD database, including 3,080 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 0.19 (3080 hom., cov: 32)
• Consequence: LOC105369677 XR_931397.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 1 publications found

Genes affected

LOC105369677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 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: 0.191 AC: 29072 AN: 152052 Hom.: 3081 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.191 AC: 29080 AN: 152170 Hom.: 3080 Cov.: 32 AF XY: 0.191 AC XY: 14210 AN XY: 74390

African (AFR) AF: 0.132 AC: 5496 AN: 41502

American (AMR) AF: 0.151 AC: 2317 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 894 AN: 3472

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5190

South Asian (SAS) AF: 0.176 AC: 846 AN: 4818

European-Finnish (FIN) AF: 0.291 AC: 3077 AN: 10570

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15794 AN: 68008

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.222 Hom.: 483

Bravo AF: 0.176

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.75
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10772967; hg19: chr12-16961000;