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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369677	XR_931397.3	n.674-20019A>T		intron_variant	Intron 5 of 5

Ensembl

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

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 v4.3

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;