ENST00000637635.1:n.350-4323G>A

Variant names:

• chr16-50489283-G-A
• rs8044151
• ENST00000637635.1:n.350-4323G>A

Variant summary

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

The ENST00000637635.1(ENSG00000260573):​n.350-4323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0746 in 152,308 control chromosomes in the GnomAD database, including 571 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 0.075 (571 hom., cov: 32)
• Consequence: ENSG00000260573 ENST00000637635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 4 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=-0.51).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0981 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.350-4323G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0747 AC: 11373 AN: 152190 Hom.: 571 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0746 AC: 11368 AN: 152308 Hom.: 571 Cov.: 32 AF XY: 0.0742 AC XY: 5527 AN XY: 74470

African (AFR) AF: 0.0219 AC: 911 AN: 41578

American (AMR) AF: 0.102 AC: 1566 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5180

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4824

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10614

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0965 AC: 6563 AN: 68020

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0919 Hom.: 2179

Bravo AF: 0.0762

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		0.67

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: rs8044151;

hg19: chr16-50523194;