rs75213930

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650063.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000650063.1		n.402-3837C>T		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.234-3837C>T		intron	N/A
	ENSG00000233290	ENST00000663002.2		n.94-3837C>T		intron	N/A

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

African (AFR) AF: 0.00957 AC: 397 AN: 41504

American (AMR) AF: 0.0404 AC: 617 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4814

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10546

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0551 AC: 3743 AN: 67968

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0308 Hom.: 20

Bravo AF: 0.0360

Asia WGS AF: 0.0110 AC: 38 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.16
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs75213930; hg19: chr1-83125608;