rs75213930

Variant names:

• chr1-82659925-G-A
• rs75213930
• ENST00000650063.1:n.402-3837C>T

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.402-3837C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 152,068 control chromosomes in the GnomAD database, including 240 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 0.045 (240 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0536 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
ENSG00000233290	ENST00000650063.1	n.402-3837C>T		intron_variant	Intron 4 of 6
ENSG00000233290	ENST00000653483.1	n.234-3837C>T		intron_variant	Intron 2 of 4
ENSG00000233290	ENST00000663002.1	n.94-3837C>T		intron_variant	Intron 1 of 3
ENSG00000233290	ENST00000702694.1	n.94-3837C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6798 AN: 151950 Hom.: 240 Cov.: 32

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0447 AC: 6796 AN: 152068 Hom.: 240 Cov.: 32 AF XY: 0.0490 AC XY: 3640 AN XY: 74326

Gnomad4 AFR AF: 0.00957

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0427 Hom.: 19

Bravo AF: 0.0360

Asia WGS AF: 0.0110 AC: 38 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75213930; hg19: chr1-83125608;