rs12720917

Variant names:

• chr16-56985480-T-C
• rs12720917
• XR_007065081.1:n.3673A>G

Variant summary

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

The XR_007065081.1(LOC124903696):​n.3673A>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 0.105 in 152,152 control chromosomes in the GnomAD database, including 1,111 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 0.10 (1111 hom., cov: 32)
• Consequence: LOC124903696 XR_007065081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 18 publications found

Genes affected

LOC124903696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15934 AN: 152034 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.105 AC: 15943 AN: 152152 Hom.: 1111 Cov.: 32 AF XY: 0.103 AC XY: 7690 AN XY: 74396

African (AFR) AF: 0.0288 AC: 1194 AN: 41518

American (AMR) AF: 0.0936 AC: 1430 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.115 AC: 557 AN: 4828

European-Finnish (FIN) AF: 0.120 AC: 1272 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10656 AN: 67990

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.138 Hom.: 1883

Bravo AF: 0.100

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.84
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs12720917; hg19: chr16-57019392;