19-4182942-G-T

Variant names:

• chr19-4182942-G-T
• rs3760905
• NM_001393985.1:c.-37+202G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393985.1(ANKRD24):​c.-37+202G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 145,024 control chromosomes in the GnomAD database, including 3,315 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 0.19 (3315 hom., cov: 31)
• Consequence: ANKRD24 NM_001393985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 27 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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD24	NM_001393985.1	c.-37+202G>T		intron_variant	Intron 1 of 21	ENST00000318934.9	NP_001380914.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD24	ENST00000318934.9	c.-37+202G>T		intron_variant	Intron 1 of 21	5	NM_001393985.1	ENSP00000321731.4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 28206 AN: 144914 Hom.: 3308 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0973

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.195 AC: 28253 AN: 145024 Hom.: 3315 Cov.: 31 AF XY: 0.204 AC XY: 14356 AN XY: 70530

African (AFR) AF: 0.236 AC: 9277 AN: 39294

American (AMR) AF: 0.273 AC: 3962 AN: 14514

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 634 AN: 3376

East Asian (EAS) AF: 0.546 AC: 2781 AN: 5096

South Asian (SAS) AF: 0.229 AC: 1073 AN: 4682

European-Finnish (FIN) AF: 0.158 AC: 1525 AN: 9632

Middle Eastern (MID) AF: 0.105 AC: 29 AN: 276

European-Non Finnish (NFE) AF: 0.129 AC: 8439 AN: 65264

Other (OTH) AF: 0.188 AC: 377 AN: 2010

Alfa AF: 0.151 Hom.: 4734

Bravo AF: 0.197

Asia WGS AF: 0.375 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-3.2
PromoterAI		0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3760905; hg19: chr19-4182939;