10-5882259-G-A

Variant names:

• chr10-5882259-G-A
• rs603780
• NM_019046.3:c.849+747C>T

Variant summary

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

The NM_019046.3(ANKRD16):​c.849+747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,786 control chromosomes in the GnomAD database, including 10,667 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 0.35 (10667 hom., cov: 30)
• Consequence: ANKRD16 NM_019046.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 2 publications found

Genes affected

ANKRD16 (HGNC:23471): (ankyrin repeat domain 16) Predicted to be involved in tRNA modification. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019046.3. 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
	ANKRD16	NM_019046.3	MANE Select	c.849+747C>T		intron	N/A	NP_061919.1
	ANKRD16	NM_001009941.3		c.849+747C>T		intron	N/A	NP_001009941.1
	ANKRD16	NM_001009943.3		c.849+747C>T		intron	N/A	NP_001009943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD16	ENST00000380094.10	TSL:2 MANE Select	c.849+747C>T		intron	N/A	ENSP00000369436.4
	ANKRD16	ENST00000380092.8	TSL:1	c.849+747C>T		intron	N/A	ENSP00000369434.4
	ANKRD16	ENST00000191063.8	TSL:3	c.849+747C>T		intron	N/A	ENSP00000352361.6

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52983 AN: 151668 Hom.: 10661 Cov.: 30

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.349 AC: 53011 AN: 151786 Hom.: 10667 Cov.: 30 AF XY: 0.358 AC XY: 26527 AN XY: 74146

African (AFR) AF: 0.166 AC: 6861 AN: 41442

American (AMR) AF: 0.477 AC: 7277 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3464 AN: 5096

South Asian (SAS) AF: 0.486 AC: 2336 AN: 4802

European-Finnish (FIN) AF: 0.424 AC: 4461 AN: 10520

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26306 AN: 67894

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.329 Hom.: 1379

Bravo AF: 0.346

Asia WGS AF: 0.501 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-1.7
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: rs603780; hg19: chr10-5924222;