chr1-217973513-G-A

Variant names:

• chr1-217973513-G-A
• rs4475815
• ENST00000848869.1:n.558-31291C>T

Variant summary

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

The ENST00000848869.1(ENSG00000286775):​n.558-31291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,888 control chromosomes in the GnomAD database, including 9,984 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 0.34 (9984 hom., cov: 32)
• Consequence: ENSG00000286775 ENST00000848869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

ENSG00000286775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372922	XR_001738466.2	n.418-31291C>T		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286775	ENST00000848869.1	n.558-31291C>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52346 AN: 151770 Hom.: 9976 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.345 AC: 52385 AN: 151888 Hom.: 9984 Cov.: 32 AF XY: 0.349 AC XY: 25917 AN XY: 74236

African (AFR) AF: 0.200 AC: 8288 AN: 41452

American (AMR) AF: 0.329 AC: 5028 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3349 AN: 5152

South Asian (SAS) AF: 0.538 AC: 2583 AN: 4798

European-Finnish (FIN) AF: 0.370 AC: 3905 AN: 10544

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26540 AN: 67896

Other (OTH) AF: 0.368 AC: 777 AN: 2112

Alfa AF: 0.359 Hom.: 21350

Bravo AF: 0.333

Asia WGS AF: 0.528 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.058
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4475815; hg19: chr1-218146855;