ENST00000848621.1:n.72+16616T>C

Variant names:

• chr1-228826680-T-C
• rs241301
• ENST00000848621.1:n.72+16616T>C

Variant summary

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

The ENST00000848621.1(ENSG00000310264):​n.72+16616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,176 control chromosomes in the GnomAD database, including 11,708 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 0.39 (11708 hom., cov: 33)
• Consequence: ENSG00000310264 ENST00000848621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310264	ENST00000848621.1	n.72+16616T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58806 AN: 152058 Hom.: 11705 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.387 AC: 58822 AN: 152176 Hom.: 11708 Cov.: 33 AF XY: 0.382 AC XY: 28425 AN XY: 74400

African (AFR) AF: 0.382 AC: 15861 AN: 41504

American (AMR) AF: 0.433 AC: 6616 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1588 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1456 AN: 5182

South Asian (SAS) AF: 0.252 AC: 1213 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3348 AN: 10604

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27261 AN: 68000

Other (OTH) AF: 0.422 AC: 890 AN: 2108

Alfa AF: 0.399 Hom.: 52306

Bravo AF: 0.397

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs241301; hg19: chr1-228962427;