4-33201518-G-A

Variant names:

• chr4-33201518-G-A
• rs10517270
• ENST00000653925.1:n.38-1162G>A

Variant summary

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

The ENST00000653925.1(ENSG00000287968):​n.38-1162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,822 control chromosomes in the GnomAD database, including 2,262 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 0.11 (2262 hom., cov: 32)
• Consequence: ENSG00000287968 ENST00000653925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 4 publications found

Genes affected

ENSG00000287968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653925.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287968	ENST00000653925.1		n.38-1162G>A		intron	N/A
	ENSG00000287968	ENST00000795184.1		n.419-12851G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15921 AN: 151706 Hom.: 2242 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0428

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.105 AC: 15987 AN: 151822 Hom.: 2262 Cov.: 32 AF XY: 0.103 AC XY: 7639 AN XY: 74212

African (AFR) AF: 0.321 AC: 13225 AN: 41242

American (AMR) AF: 0.0428 AC: 653 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5164

South Asian (SAS) AF: 0.0784 AC: 378 AN: 4820

European-Finnish (FIN) AF: 0.0231 AC: 244 AN: 10574

Middle Eastern (MID) AF: 0.0690 AC: 20 AN: 290

European-Non Finnish (NFE) AF: 0.0171 AC: 1161 AN: 67968

Other (OTH) AF: 0.0799 AC: 169 AN: 2116

Alfa AF: 0.0397 Hom.: 2334

Bravo AF: 0.116

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.97
DANN	Benign	0.48
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10517270; hg19: chr4-33203140;