rs130650

Variant names:

• chr22-39248517-C-T
• rs130650
• ENST00000641466.3:n.76-1633C>T

Variant summary

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

The ENST00000641466.3(ENSG00000284633):​n.76-1633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,182 control chromosomes in the GnomAD database, including 3,351 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 0.20 (3351 hom., cov: 31)
• Consequence: ENSG00000284633 ENST00000641466.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 4 publications found

Genes affected

ENSG00000284633 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 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
ENSG00000284633	ENST00000641466.3	n.76-1633C>T		intron_variant	Intron 1 of 1
ENSG00000284633	ENST00000641859.1	n.109+6221C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30557 AN: 152064 Hom.: 3350 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0288

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.201 AC: 30558 AN: 152182 Hom.: 3351 Cov.: 31 AF XY: 0.197 AC XY: 14683 AN XY: 74398

African (AFR) AF: 0.148 AC: 6152 AN: 41520

American (AMR) AF: 0.192 AC: 2931 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3468

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5190

South Asian (SAS) AF: 0.314 AC: 1508 AN: 4810

European-Finnish (FIN) AF: 0.163 AC: 1729 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16544 AN: 67992

Other (OTH) AF: 0.197 AC: 415 AN: 2110

Alfa AF: 0.223 Hom.: 825

Bravo AF: 0.199

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs130650; hg19: chr22-39644522;