1-8153367-T-C

Variant names:

• chr1-8153367-T-C
• rs4908739
• ENST00000777658.1:n.155-1362T>C

Variant summary

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

The ENST00000777658.1(ERRFI1-DT):​n.155-1362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,112 control chromosomes in the GnomAD database, including 42,645 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 0.74 (42645 hom., cov: 32)
• Consequence: ERRFI1-DT ENST00000777658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERRFI1-DT	ENST00000777658.1		n.155-1362T>C		intron	N/A
	ERRFI1-DT	ENST00000777659.1		n.764+901T>C		intron	N/A
	ERRFI1-DT	ENST00000777660.1		n.159-1362T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112512 AN: 151994 Hom.: 42570 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.741 AC: 112640 AN: 152112 Hom.: 42645 Cov.: 32 AF XY: 0.737 AC XY: 54813 AN XY: 74356

African (AFR) AF: 0.904 AC: 37524 AN: 41528

American (AMR) AF: 0.799 AC: 12210 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2640 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3874 AN: 5164

South Asian (SAS) AF: 0.646 AC: 3112 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6121 AN: 10542

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44778 AN: 67988

Other (OTH) AF: 0.759 AC: 1603 AN: 2112

Alfa AF: 0.646 Hom.: 2581

Bravo AF: 0.765

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.22
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4908739; hg19: chr1-8213427; COSMIC: COSV69612790;