16-79246401-C-T

Position:

• chr16-79246401-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024450279.2(MAF):​c.*29-33500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,952 control chromosomes in the GnomAD database, including 2,266 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 0.14 (2266 hom., cov: 30)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*29-33500G>A		intron_variant
MAF	XR_001751902.3	n.2016-33500G>A		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2016-33500G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21315 AN: 151834 Hom.: 2261 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.140 AC: 21344 AN: 151952 Hom.: 2266 Cov.: 30 AF XY: 0.140 AC XY: 10371 AN XY: 74262

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.0544

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0788 Hom.: 815

Bravo AF: 0.143

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9922579; hg19: chr16-79280298;