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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903696	XR_007065081.1	n.3673A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

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 v4.3

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;