1-8162022-C-T

Variant names:

• chr1-8162022-C-T
• rs4908741
• ENST00000777658.1:n.339+7109C>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.339+7109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,062 control chromosomes in the GnomAD database, including 47,185 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 0.78 (47185 hom., cov: 30)
• Consequence: ERRFI1-DT ENST00000777658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 2 publications found

Genes affected

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

LINC01714 (HGNC:52501): (long intergenic non-protein coding RNA 1714)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 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.339+7109C>T		intron	N/A
	LINC01714	ENST00000777791.1		n.172+3156C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118891 AN: 151942 Hom.: 47122 Cov.: 30

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.783 AC: 119012 AN: 152062 Hom.: 47185 Cov.: 30 AF XY: 0.783 AC XY: 58148 AN XY: 74298

African (AFR) AF: 0.918 AC: 38119 AN: 41502

American (AMR) AF: 0.824 AC: 12556 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4147 AN: 5166

South Asian (SAS) AF: 0.720 AC: 3473 AN: 4822

European-Finnish (FIN) AF: 0.697 AC: 7365 AN: 10560

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48147 AN: 67984

Other (OTH) AF: 0.791 AC: 1673 AN: 2114

Alfa AF: 0.769 Hom.: 6660

Bravo AF: 0.800

Asia WGS AF: 0.757 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.17
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4908741; hg19: chr1-8222082;