4-4931098-A-G

Variant names:

• chr4-4931098-A-G
• rs7678151
• ENST00000774609.1:n.142-2722A>G

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.142-2722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,972 control chromosomes in the GnomAD database, including 36,609 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 0.69 (36609 hom., cov: 31)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774609.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928306	NR_125893.1		n.354-2722A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300857	ENST00000774609.1		n.142-2722A>G		intron	N/A
	ENSG00000300857	ENST00000774610.1		n.165-2722A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104785 AN: 151854 Hom.: 36548 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.690 AC: 104901 AN: 151972 Hom.: 36609 Cov.: 31 AF XY: 0.700 AC XY: 51973 AN XY: 74276

African (AFR) AF: 0.755 AC: 31281 AN: 41430

American (AMR) AF: 0.762 AC: 11643 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4641 AN: 5162

South Asian (SAS) AF: 0.725 AC: 3493 AN: 4818

European-Finnish (FIN) AF: 0.729 AC: 7691 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42068 AN: 67968

Other (OTH) AF: 0.688 AC: 1450 AN: 2108

Alfa AF: 0.679 Hom.: 57950

Bravo AF: 0.695

Asia WGS AF: 0.817 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs7678151; hg19: chr4-4932825;