16-84287168-T-C

Variant names:

• chr16-84287168-T-C
• rs11865624
• XM_047435022.1:c.-406+499T>C

Variant summary

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

The XM_047435022.1(LOC124903734):​c.-406+499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,154 control chromosomes in the GnomAD database, including 3,199 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 0.17 (3199 hom., cov: 32)
• Consequence: LOC124903734 XM_047435022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 5 publications found

Genes affected

LOC124903734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.171 AC: 25995 AN: 152036 Hom.: 3188 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0740

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.171 AC: 26049 AN: 152154 Hom.: 3199 Cov.: 32 AF XY: 0.178 AC XY: 13254 AN XY: 74394

African (AFR) AF: 0.319 AC: 13218 AN: 41474

American (AMR) AF: 0.205 AC: 3142 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0740 AC: 257 AN: 3472

East Asian (EAS) AF: 0.187 AC: 967 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2309 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4768 AN: 68022

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.0939 Hom.: 2883

Bravo AF: 0.177

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.21
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11865624; hg19: chr16-84320774;