16-71600908-A-T

Variant names:

• chr16-71600908-A-T
• rs4788815
• XR_933717.2:n.239+10866T>A

Variant summary

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

The XR_933717.2(LOC105371334):​n.239+10866T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,044 control chromosomes in the GnomAD database, including 36,028 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 0.69 (36028 hom., cov: 31)
• Consequence: LOC105371334 XR_933717.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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: 0.685 AC: 104125 AN: 151926 Hom.: 35992 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.685 AC: 104217 AN: 152044 Hom.: 36028 Cov.: 31 AF XY: 0.687 AC XY: 51047 AN XY: 74298

African (AFR) AF: 0.767 AC: 31829 AN: 41480

American (AMR) AF: 0.701 AC: 10703 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2246 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4040 AN: 5154

South Asian (SAS) AF: 0.561 AC: 2703 AN: 4814

European-Finnish (FIN) AF: 0.676 AC: 7151 AN: 10580

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43457 AN: 67976

Other (OTH) AF: 0.646 AC: 1362 AN: 2108

Alfa AF: 0.657 Hom.: 4104

Bravo AF: 0.694

Asia WGS AF: 0.645 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4788815; hg19: chr16-71634811;