rs921048

Variant names:

• chr13-24752041-G-C
• rs921048
• XM_011535152.3:c.-1064G>C

Variant summary

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

The ENST00000662637.2(ENSG00000287887):​n.848G>C 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: ENSG00000287887 ENST00000662637.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 2 publications found

Genes affected

RNF17 (HGNC:10060): (ring finger protein 17) This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]

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

ENSG00000287887 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662637.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD20A10P	ENST00000457591.1	TSL:6	n.131C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000287887	ENST00000662637.2		n.848G>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000287887	ENST00000831829.1		n.223+4107G>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 12 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.357 AC: 14787 AN: 41454

American (AMR) AF: 0.403 AC: 6169 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.147 AC: 762 AN: 5184

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4810

European-Finnish (FIN) AF: 0.446 AC: 4719 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32677 AN: 67984

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs921048;

hg19: chr13-25326179;