16-79475437-T-C

Position:

• chr16-79475437-T-C

Variant summary

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

The XM_024450279.2(MAF):​c.*28+110443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,546 control chromosomes in the GnomAD database, including 2,287 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 0.16 (2287 hom., cov: 30)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAF	XM_024450279.2	c.*28+110443A>G		intron_variant			XP_024306047.1
MAF	XR_001751902.3	n.2015+110443A>G		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2015+110443A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24322 AN: 151432 Hom.: 2285 Cov.: 30

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.160 AC: 24321 AN: 151546 Hom.: 2287 Cov.: 30 AF XY: 0.162 AC XY: 12006 AN XY: 73992

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.171

Alfa AF: 0.173 Hom.: 4931

Bravo AF: 0.164

Asia WGS AF: 0.241 AC: 839 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4888984; hg19: chr16-79509334;