rs4908736

Variant names:

• chr1-8127151-A-G
• rs4908736
• ENST00000777658.1:n.155-27578A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-8127151-A-G
• chr1-8127151-A-T

Variant summary

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

The ENST00000777658.1(ERRFI1-DT):​n.155-27578A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,752 control chromosomes in the GnomAD database, including 5,504 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 0.22 (5504 hom., cov: 33)
• Consequence: ERRFI1-DT ENST00000777658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 10 publications found

Genes affected

ERRFI1-DT (HGNC:55646): (ERRFI1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777658.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERRFI1-DT	NR_185980.1		n.*81A>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERRFI1-DT	ENST00000777658.1		n.155-27578A>G		intron	N/A
	ERRFI1-DT	ENST00000777659.1		n.653-25204A>G		intron	N/A
	ERRFI1-DT	ENST00000777660.1		n.159-27578A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33177 AN: 151638 Hom.: 5486 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.219 AC: 33240 AN: 151752 Hom.: 5504 Cov.: 33 AF XY: 0.225 AC XY: 16673 AN XY: 74214

African (AFR) AF: 0.308 AC: 12637 AN: 41050

American (AMR) AF: 0.358 AC: 5466 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.695 AC: 3596 AN: 5174

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4826

European-Finnish (FIN) AF: 0.0824 AC: 875 AN: 10618

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8392 AN: 68018

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.158 Hom.: 12366

Bravo AF: 0.246

Asia WGS AF: 0.448 AC: 1555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.35
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4908736;

hg19: chr1-8187211;