chr13-24752041-G-C

Position:

• chr13-24752041-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457591.1(ANKRD20A10P):​n.131C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,116 control chromosomes in the GnomAD database, including 14,146 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 0.42 (14142 hom., cov: 33)
  • Exomes 𝑓: 0.41 (4 hom.)
• Consequence: ANKRD20A10P ENST00000457591.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

ANKRD20A10P (HGNC:39707): (ankyrin repeat domain 20 family member A10, pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNF17	XM_011535152.3	c.-1064G>C		5_prime_UTR_variant	3/41
RNF17	XM_011535156.3	c.-1064G>C		5_prime_UTR_variant	3/41
RNF17	XM_011535157.3	c.-1064G>C		5_prime_UTR_variant	3/41

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD20A10P	ENST00000457591.1	n.131C>G		non_coding_transcript_exon_variant	1/1
	ENST00000662637.1	n.799G>C		non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64489 AN: 151962 Hom.: 14131 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.452

GnomAD4 exome AF: 0.412 AC: 14 AN: 34 Hom.: 4 Cov.: 0 AF XY: 0.400 AC XY: 8 AN XY: 20

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.424 AC: 64535 AN: 152082 Hom.: 14142 Cov.: 33 AF XY: 0.421 AC XY: 31283 AN XY: 74346

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.456

Alfa AF: 0.441 Hom.: 1862

Bravo AF: 0.418

Asia WGS AF: 0.338 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921048; hg19: chr13-25326179;