ENST00000848621.1:n.73-49218T>G

Variant names:

• chr1-228862088-T-G
• rs801114
• ENST00000848621.1:n.73-49218T>G

Variant summary

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

The ENST00000848621.1(ENSG00000310264):​n.73-49218T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,018 control chromosomes in the GnomAD database, including 19,602 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 0.47 (19602 hom., cov: 32)
• Consequence: ENSG00000310264 ENST00000848621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 40 publications found

Genes affected

ENSG00000310264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848621.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310264	ENST00000848621.1		n.73-49218T>G		intron	N/A
	ENSG00000310285	ENST00000848808.1		n.213-3351A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72020 AN: 151900 Hom.: 19553 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.474 AC: 72118 AN: 152018 Hom.: 19602 Cov.: 32 AF XY: 0.471 AC XY: 34999 AN XY: 74292

African (AFR) AF: 0.753 AC: 31231 AN: 41466

American (AMR) AF: 0.462 AC: 7063 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5162

South Asian (SAS) AF: 0.288 AC: 1391 AN: 4824

European-Finnish (FIN) AF: 0.336 AC: 3548 AN: 10554

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23882 AN: 67958

Other (OTH) AF: 0.484 AC: 1020 AN: 2106

Alfa AF: 0.392 Hom.: 55902

Bravo AF: 0.498

Asia WGS AF: 0.386 AC: 1343 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	1.6
DANN	Benign	0.43
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs801114; hg19: chr1-228997835;