19-4190873-G-A

Variant names:

• chr19-4190873-G-A
• rs352500
• NM_001393985.1:c.36+4412G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ANKRD24 Gene-Disease associations (from GenCC):

• sensorineural hearing loss disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000306086 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393985.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD24	NM_001393985.1	MANE Select	c.36+4412G>A		intron	N/A	NP_001380914.1
	ANKRD24	NM_001393552.1		c.36+4412G>A		intron	N/A	NP_001380481.1
	ANKRD24	NM_001393553.1		c.36+4412G>A		intron	N/A	NP_001380482.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD24	ENST00000318934.9	TSL:5 MANE Select	c.36+4412G>A		intron	N/A	ENSP00000321731.4
	ANKRD24	ENST00000597689.5	TSL:1	c.36+4412G>A		intron	N/A	ENSP00000470227.1
	ANKRD24	ENST00000600132.5	TSL:5	c.36+4412G>A		intron	N/A	ENSP00000471252.1

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

African (AFR) AF: 0.666 AC: 27625 AN: 41486

American (AMR) AF: 0.377 AC: 5765 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5176

South Asian (SAS) AF: 0.462 AC: 2227 AN: 4824

European-Finnish (FIN) AF: 0.457 AC: 4824 AN: 10566

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33583 AN: 67992

Other (OTH) AF: 0.502 AC: 1062 AN: 2114

Alfa AF: 0.499 Hom.: 15545

Bravo AF: 0.519

Asia WGS AF: 0.378 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.20
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs352500; hg19: chr19-4190870;