16-79539854-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.*28+46026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,238 control chromosomes in the GnomAD database, including 59,597 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 0.88 (59597 hom., cov: 33)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*28+46026G>A		intron_variant
MAF	XR_001751902.3	n.2015+46026G>A		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2015+46026G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133803 AN: 152120 Hom.: 59580 Cov.: 33

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.879 AC: 133861 AN: 152238 Hom.: 59597 Cov.: 33 AF XY: 0.878 AC XY: 65376 AN XY: 74442

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.886

Alfa AF: 0.941 Hom.: 127467

Bravo AF: 0.859

Asia WGS AF: 0.864 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.25
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs190369; hg19: chr16-79573751;