16-79382666-C-T

Position:

• chr16-79382666-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.*29-169765G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,112 control chromosomes in the GnomAD database, including 11,461 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 0.31 (11461 hom., cov: 33)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*29-169765G>A		intron_variant
MAF	XR_001751902.3	n.2016-169765G>A		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2016-169765G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47552 AN: 151996 Hom.: 11407 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.313 AC: 47676 AN: 152112 Hom.: 11461 Cov.: 33 AF XY: 0.312 AC XY: 23223 AN XY: 74352

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.262

Alfa AF: 0.162 Hom.: 3768

Bravo AF: 0.331

Asia WGS AF: 0.349 AC: 1210 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7192960; hg19: chr16-79416563;