ENST00000774609.1:n.267+7784A>G

Variant names:

• chr4-4941729-A-G
• rs755927
• ENST00000774609.1:n.267+7784A>G

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.267+7784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,236 control chromosomes in the GnomAD database, including 1,504 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 0.11 (1504 hom., cov: 32)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 3 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928306	NR_125893.1	n.479+7784A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300857	ENST00000774609.1	n.267+7784A>G		intron_variant	Intron 3 of 8
ENSG00000300857	ENST00000774610.1	n.290+7784A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16892 AN: 152118 Hom.: 1498 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.111 AC: 16920 AN: 152236 Hom.: 1504 Cov.: 32 AF XY: 0.113 AC XY: 8398 AN XY: 74432

African (AFR) AF: 0.235 AC: 9771 AN: 41534

American (AMR) AF: 0.0677 AC: 1036 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.192 AC: 992 AN: 5176

South Asian (SAS) AF: 0.0983 AC: 474 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3016 AN: 68014

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.0891 Hom.: 175

Bravo AF: 0.113

Asia WGS AF: 0.176 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.74
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs755927; hg19: chr4-4943456;