rs2549513

chr16-79516830-C-Achr16-79516830-C-Gchr16-79516830-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+69050G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,170 control chromosomes in the GnomAD database, including 53,563 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 0.84 (53563 hom., cov: 32)
• Consequence: MAF XM_024450279.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

MAF (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAF	XM_024450279.2	c.*28+69050G>T		intron_variant
MAF	XR_001751902.3	n.2015+69050G>T		intron_variant, non_coding_transcript_variant
MAF	XR_002957802.2	n.2015+69050G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127249 AN: 152052 Hom.: 53525 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.837 AC: 127341 AN: 152170 Hom.: 53563 Cov.: 32 AF XY: 0.838 AC XY: 62378 AN XY: 74412

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.850

Alfa AF: 0.862 Hom.: 67403

Bravo AF: 0.838

Asia WGS AF: 0.899 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.84
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2549513; hg19: chr16-79550727;