rs5757091

chr22-38424590-G-Cchr22-38424590-G-T

Variant summary

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

The ENST00000433230.1(ENSG00000228620):n.136+167G>C 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 0.0463 in 152,220 control chromosomes in the GnomAD database, including 392 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 0.046 (392 hom., cov: 32)
• Consequence: ENST00000433230.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927183	XR_938252.3	n.146+167G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000433230.1	n.136+167G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7038 AN: 152102 Hom.: 387 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00885

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0463 AC: 7055 AN: 152220 Hom.: 392 Cov.: 32 AF XY: 0.0485 AC XY: 3609 AN XY: 74420

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.00887

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0283 Hom.: 20

Bravo AF: 0.0559

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.70
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5757091; hg19: chr22-38820595;