rs925570

Positions:

• chr4-22023973-T-C

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.446-35111T>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 0.689 in 152,074 control chromosomes in the GnomAD database, including 38,073 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 0.69 (38073 hom., cov: 33)
• Consequence: ENST00000510705.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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
	ENST00000510705.3	n.446-35111T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104744 AN: 151956 Hom.: 38053 Cov.: 33

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.689 AC: 104802 AN: 152074 Hom.: 38073 Cov.: 33 AF XY: 0.695 AC XY: 51627 AN XY: 74322

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.704

Alfa AF: 0.700 Hom.: 5584

Bravo AF: 0.678

Asia WGS AF: 0.675 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925570; hg19: chr4-22025596;