rs4359565

chr19-4183685-A-Gchr19-4183685-A-T

Variant summary

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

The NM_001393985.1(ANKRD24):c.-37+945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,072 control chromosomes in the GnomAD database, including 732 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 0.065 (732 hom., cov: 31)
• Consequence: ANKRD24 NM_001393985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

Genes affected

ANKRD24 (HGNC:29424): (ankyrin repeat domain 24)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD24	NM_001393985.1	c.-37+945A>G		intron_variant		ENST00000318934.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD24	ENST00000318934.9	c.-37+945A>G		intron_variant		5	NM_001393985.1	A2
ANKRD24	ENST00000600132.5	c.-153+208A>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9782 AN: 151954 Hom.: 729 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0646 AC: 9821 AN: 152072 Hom.: 732 Cov.: 31 AF XY: 0.0675 AC XY: 5018 AN XY: 74348

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00909

Gnomad4 OTH AF: 0.0602

Alfa AF: 0.0380 Hom.: 49

Bravo AF: 0.0713

Asia WGS AF: 0.164 AC: 569 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	0.41
Dann	Benign	0.097

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4359565; hg19: chr19-4183682;