1-34285335-T-C

Variant names:

• chr1-34285335-T-C
• rs771390
• ENST00000788214.1:n.400+18552T>C

Variant summary

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

The ENST00000788214.1(ENSG00000302624):​n.400+18552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,102 control chromosomes in the GnomAD database, including 48,575 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 0.80 (48575 hom., cov: 31)
• Consequence: ENSG00000302624 ENST00000788214.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 5 publications found

Genes affected

ENSG00000302624 (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 = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378639	XR_947169.2	n.493+4328T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302624	ENST00000788214.1	n.400+18552T>C		intron_variant	Intron 1 of 2
ENSG00000302624	ENST00000788215.1	n.220-7594T>C		intron_variant	Intron 1 of 2
ENSG00000302624	ENST00000788216.1	n.540+4328T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121250 AN: 151984 Hom.: 48523 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.798 AC: 121362 AN: 152102 Hom.: 48575 Cov.: 31 AF XY: 0.802 AC XY: 59639 AN XY: 74336

African (AFR) AF: 0.827 AC: 34305 AN: 41504

American (AMR) AF: 0.800 AC: 12218 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2497 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4515 AN: 5160

South Asian (SAS) AF: 0.846 AC: 4069 AN: 4810

European-Finnish (FIN) AF: 0.801 AC: 8476 AN: 10584

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.773 AC: 52580 AN: 67990

Other (OTH) AF: 0.784 AC: 1653 AN: 2108

Alfa AF: 0.783 Hom.: 89145

Bravo AF: 0.801

Asia WGS AF: 0.848 AC: 2949 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	4.1
DANN	Benign	0.48
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs771390; hg19: chr1-34750936;