chr16-71619734-A-G

Variant names:

• chr16-71619734-A-G
• rs2334880
• XR_933717.2:n.103+1545T>C

Variant summary

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

The XR_933717.2(LOC105371334):​n.103+1545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,200 control chromosomes in the GnomAD database, including 49,571 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 0.80 (49571 hom., cov: 33)
• Consequence: LOC105371334 XR_933717.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 20 publications found

Genes affected

LOC105371334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.800 AC: 121675 AN: 152082 Hom.: 49562 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.800 AC: 121711 AN: 152200 Hom.: 49571 Cov.: 33 AF XY: 0.806 AC XY: 60016 AN XY: 74418

African (AFR) AF: 0.638 AC: 26475 AN: 41496

American (AMR) AF: 0.889 AC: 13586 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5133 AN: 5182

South Asian (SAS) AF: 0.965 AC: 4661 AN: 4828

European-Finnish (FIN) AF: 0.874 AC: 9266 AN: 10606

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56668 AN: 68014

Other (OTH) AF: 0.837 AC: 1768 AN: 2112

Alfa AF: 0.789 Hom.: 25016

Bravo AF: 0.794

Asia WGS AF: 0.943 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.66
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2334880; hg19: chr16-71653637;