XR_007065081.1:n.2738G>C

Variant names:

• chr16-56986415-C-G
• rs17369163
• XR_007065081.1:n.2738G>C

Variant summary

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

The XR_007065081.1(LOC124903696):​n.2738G>C 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 0.0909 in 152,252 control chromosomes in the GnomAD database, including 905 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 0.091 (905 hom., cov: 32)
• Consequence: LOC124903696 XR_007065081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 9 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0910 AC: 13846 AN: 152134 Hom.: 905 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0909 AC: 13846 AN: 152252 Hom.: 905 Cov.: 32 AF XY: 0.0918 AC XY: 6838 AN XY: 74448

African (AFR) AF: 0.0203 AC: 843 AN: 41574

American (AMR) AF: 0.0893 AC: 1367 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4832

European-Finnish (FIN) AF: 0.193 AC: 2045 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8607 AN: 67996

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.116 Hom.: 621

Bravo AF: 0.0814

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs17369163; hg19: chr16-57020327;