rs10517270

Positions:

• chr4-33201518-G-A
• chr4-33201518-G-T

Variant summary

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

The ENST00000653925.1(ENSG00000287968):​n.38-1162G>A variant causes a intron, non coding transcript 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: ENST00000653925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653925.1	n.38-1162G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0799

Alfa AF: 0.0268 Hom.: 464

Bravo AF: 0.116

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517270; hg19: chr4-33203140;