chr16-50465933-G-A

Variant names:

• chr16-50465933-G-A
• rs1861545
• ENST00000637635.1:n.350-27673G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637635.1(ENSG00000260573):​n.350-27673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,200 control chromosomes in the GnomAD database, including 47,547 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 0.79 (47547 hom., cov: 33)
• Consequence: ENSG00000260573 ENST00000637635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 3 publications found

Genes affected

ENSG00000260573 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260573	ENST00000637635.1	n.350-27673G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119936 AN: 152082 Hom.: 47505 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.789 AC: 120038 AN: 152200 Hom.: 47547 Cov.: 33 AF XY: 0.796 AC XY: 59250 AN XY: 74404

African (AFR) AF: 0.770 AC: 31963 AN: 41516

American (AMR) AF: 0.830 AC: 12691 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2505 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5105 AN: 5166

South Asian (SAS) AF: 0.843 AC: 4063 AN: 4822

European-Finnish (FIN) AF: 0.863 AC: 9152 AN: 10608

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51947 AN: 68006

Other (OTH) AF: 0.782 AC: 1650 AN: 2110

Alfa AF: 0.770 Hom.: 9159

Bravo AF: 0.784

Asia WGS AF: 0.889 AC: 3092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.32
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1861545; hg19: chr16-50499844;