rs666788

Variant names:

• chr5-41579365-A-G
• rs666788
• ENST00000742936.1:n.104+1908A>G

Variant summary

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

The ENST00000742936.1(ENSG00000296840):​n.104+1908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,198 control chromosomes in the GnomAD database, including 938 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 0.10 (938 hom., cov: 32)
• Consequence: ENSG00000296840 ENST00000742936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 3 publications found

Genes affected

ENSG00000296840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000296840	ENST00000742936.1	n.104+1908A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15596 AN: 152078 Hom.: 935 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15601 AN: 152198 Hom.: 938 Cov.: 32 AF XY: 0.0997 AC XY: 7418 AN XY: 74412

African (AFR) AF: 0.177 AC: 7322 AN: 41484

American (AMR) AF: 0.0841 AC: 1286 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3468

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5178

South Asian (SAS) AF: 0.0620 AC: 299 AN: 4824

European-Finnish (FIN) AF: 0.0466 AC: 495 AN: 10616

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0802 AC: 5456 AN: 68016

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.101 Hom.: 163

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs666788; hg19: chr5-41579467;