rs4803750

Variant names:

• chr19-44744370-A-G
• rs4803750
• ENST00000790564.1:n.157-675A>G

Variant summary

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

The ENST00000790564.1(ENSG00000288773):​n.157-675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 151,814 control chromosomes in the GnomAD database, including 548 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 0.078 (548 hom., cov: 32)
• Consequence: ENSG00000288773 ENST00000790564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 64 publications found

Genes affected

ENSG00000288773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 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
ENSG00000288773	ENST00000790564.1	n.157-675A>G		intron_variant	Intron 1 of 2
ENSG00000288773	ENST00000790569.1	n.365-675A>G		intron_variant	Intron 3 of 4
ENSG00000288773	ENST00000790570.1	n.217-675A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11823 AN: 151714 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0779 AC: 11830 AN: 151814 Hom.: 548 Cov.: 32 AF XY: 0.0784 AC XY: 5816 AN XY: 74198

African (AFR) AF: 0.0802 AC: 3325 AN: 41454

American (AMR) AF: 0.125 AC: 1910 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.0728 AC: 377 AN: 5178

South Asian (SAS) AF: 0.157 AC: 754 AN: 4802

European-Finnish (FIN) AF: 0.0521 AC: 543 AN: 10430

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0648 AC: 4402 AN: 67940

Other (OTH) AF: 0.0657 AC: 138 AN: 2102

Alfa AF: 0.0737 Hom.: 1012

Bravo AF: 0.0836

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.80
DANN	Benign	0.81
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4803750; hg19: chr19-45247627;