rs225132

Positions:

• chr1-8035440-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445300.1(ERRFI1-DT):​n.815+6083T>G variant causes a intron, non coding transcript 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 ENST00000445300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERRFI1-DT	XR_007065452.1	n.2865+6083T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERRFI1-DT	ENST00000445300.1	n.815+6083T>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.232

Alfa AF: 0.195 Hom.: 7230

Bravo AF: 0.292

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225132; hg19: chr1-8095500;