16-50474190-A-G

Variant names:

• chr16-50474190-A-G
• rs6500315
• ENST00000637635.1:n.350-19416A>G

Variant summary

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

The ENST00000637635.1(ENSG00000260573):​n.350-19416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,168 control chromosomes in the GnomAD database, including 46,974 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 0.78 (46974 hom., cov: 32)
• Consequence: ENSG00000260573 ENST00000637635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 9 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637635.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260573	ENST00000637635.1	TSL:5	n.350-19416A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119112 AN: 152050 Hom.: 46944 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.783 AC: 119201 AN: 152168 Hom.: 46974 Cov.: 32 AF XY: 0.791 AC XY: 58811 AN XY: 74386

African (AFR) AF: 0.723 AC: 29998 AN: 41490

American (AMR) AF: 0.834 AC: 12752 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5102 AN: 5172

South Asian (SAS) AF: 0.816 AC: 3932 AN: 4820

European-Finnish (FIN) AF: 0.861 AC: 9123 AN: 10590

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52966 AN: 68014

Other (OTH) AF: 0.787 AC: 1663 AN: 2114

Alfa AF: 0.785 Hom.: 14634

Bravo AF: 0.778

Asia WGS AF: 0.876 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.075

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6500315;

hg19: chr16-50508101;