rs352500

Positions:

• chr19-4190873-G-A

Variant summary

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

The NM_001393985.1(ANKRD24):​c.36+4412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,126 control chromosomes in the GnomAD database, including 21,377 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 0.52 (21377 hom., cov: 33)
• Consequence: ANKRD24 NM_001393985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD24	NM_001393985.1	c.36+4412G>A		intron_variant		ENST00000318934.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD24	ENST00000318934.9	c.36+4412G>A		intron_variant		5	NM_001393985.1	A2
ANKRD24	ENST00000597689.5	c.36+4412G>A		intron_variant		1
ANKRD24	ENST00000600132.5	c.36+4412G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78983 AN: 152008 Hom.: 21346 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.520 AC: 79062 AN: 152126 Hom.: 21377 Cov.: 33 AF XY: 0.512 AC XY: 38084 AN XY: 74368

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.502

Alfa AF: 0.501 Hom.: 11364

Bravo AF: 0.519

Asia WGS AF: 0.378 AC: 1319 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	0.038
DANN	Benign	0.20

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: rs352500; hg19: chr19-4190870;