ENST00000476620.1:c.-37-44067A>G

Variant names:

• chr7-37904773-A-G
• rs17236800
• ENST00000476620.1:c.-37-44067A>G

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-37-44067A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,260 control chromosomes in the GnomAD database, including 1,735 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 0.14 (1735 hom., cov: 32)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• Publications: 11 publications found

Genes affected

ENSG00000290149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 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
ENSG00000290149	ENST00000476620.1	c.-37-44067A>G		intron_variant	Intron 2 of 3	4		ENSP00000425858.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21643 AN: 152140 Hom.: 1733 Cov.: 32

Gnomad AFR AF: 0.0826

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.142 AC: 21653 AN: 152260 Hom.: 1735 Cov.: 32 AF XY: 0.139 AC XY: 10334 AN XY: 74438

African (AFR) AF: 0.0825 AC: 3431 AN: 41574

American (AMR) AF: 0.117 AC: 1788 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3468

East Asian (EAS) AF: 0.0619 AC: 321 AN: 5182

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4824

European-Finnish (FIN) AF: 0.185 AC: 1958 AN: 10582

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12547 AN: 68014

Other (OTH) AF: 0.147 AC: 311 AN: 2116

Alfa AF: 0.168 Hom.: 3884

Bravo AF: 0.134

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.7
DANN	Benign	0.91
PhyloP100		0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17236800; hg19: chr7-37944375;