1-8035440-T-G

Variant names:

• chr1-8035440-T-G
• rs225132
• ENST00000445300.2:n.848+6083T>G

Variant summary

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

The ENST00000445300.2(ERRFI1-DT):​n.848+6083T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,950 control chromosomes in the GnomAD database, including 6,722 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 0.27 (6722 hom., cov: 30)
• Consequence: ERRFI1-DT ENST00000445300.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 22 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445300.2. 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
	ERRFI1-DT	NR_185980.1		n.1060+6083T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERRFI1-DT	ENST00000445300.2	TSL:2	n.848+6083T>G		intron	N/A
	ERRFI1-DT	ENST00000777653.1		n.633+6083T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41184 AN: 151832 Hom.: 6701 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.271 AC: 41254 AN: 151950 Hom.: 6722 Cov.: 30 AF XY: 0.277 AC XY: 20565 AN XY: 74272

African (AFR) AF: 0.379 AC: 15689 AN: 41412

American (AMR) AF: 0.359 AC: 5485 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3233 AN: 5126

South Asian (SAS) AF: 0.136 AC: 655 AN: 4824

European-Finnish (FIN) AF: 0.293 AC: 3091 AN: 10552

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12088 AN: 67968

Other (OTH) AF: 0.232 AC: 490 AN: 2116

Alfa AF: 0.210 Hom.: 12948

Bravo AF: 0.292

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.46
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs225132; hg19: chr1-8095500;