4-73342482-A-G

Variant names:

• chr4-73342482-A-G
• rs714825
• ENST00000835865.1:n.525-7290A>G

Variant summary

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

The ENST00000835865.1(ANKRD17-DT):​n.525-7290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,008 control chromosomes in the GnomAD database, including 12,982 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 0.41 (12982 hom., cov: 32)
• Consequence: ANKRD17-DT ENST00000835865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 3 publications found

Genes affected

ANKRD17-DT (HGNC:55556): (ANKRD17 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD17-DT	NR_187399.1	n.488-7290A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD17-DT	ENST00000835865.1	n.525-7290A>G		intron_variant	Intron 1 of 2
ANKRD17-DT	ENST00000835866.1	n.335-10862A>G		intron_variant	Intron 1 of 1
ANKRD17-DT	ENST00000835867.1	n.334-7290A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61872 AN: 151890 Hom.: 12972 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.407 AC: 61920 AN: 152008 Hom.: 12982 Cov.: 32 AF XY: 0.413 AC XY: 30656 AN XY: 74298

African (AFR) AF: 0.364 AC: 15083 AN: 41466

American (AMR) AF: 0.520 AC: 7952 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2321 AN: 5156

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4367 AN: 10552

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26661 AN: 67940

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.413 Hom.: 16678

Bravo AF: 0.415

Asia WGS AF: 0.488 AC: 1692 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs714825; hg19: chr4-74208199;