chr10-5876469-G-A

Variant names:

• chr10-5876469-G-A
• rs17145612
• NM_019046.3:c.*33+1628C>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.*33+1628C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,290 control chromosomes in the GnomAD database, including 90 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 0.022 (90 hom., cov: 33)
• Consequence: ANKRD16 NM_019046.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0958 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.*33+1628C>T		intron	N/A	NP_061919.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD16	ENST00000380094.10	TSL:2 MANE Select	c.*33+1628C>T		intron	N/A	ENSP00000369436.4

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3312 AN: 152172 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0218 AC: 3313 AN: 152290 Hom.: 90 Cov.: 33 AF XY: 0.0230 AC XY: 1716 AN XY: 74466

African (AFR) AF: 0.0118 AC: 489 AN: 41562

American (AMR) AF: 0.0138 AC: 211 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.103 AC: 534 AN: 5184

South Asian (SAS) AF: 0.0817 AC: 394 AN: 4824

European-Finnish (FIN) AF: 0.0141 AC: 150 AN: 10604

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0198 AC: 1346 AN: 68036

Other (OTH) AF: 0.0237 AC: 50 AN: 2114

Alfa AF: 0.0216 Hom.: 94

Bravo AF: 0.0207

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.63
PhyloP100		-0.60
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: rs17145612; hg19: chr10-5918432;