rs554995

Variant names:

• chr18-14180713-T-A
• rs554995
• ENST00000431648.8:n.203+1116T>A

Your query was ambiguous. Multiple possible variants found:

• chr18-14180713-T-A
• chr18-14180713-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000581935.5(ANKRD20A5P):​n.501+1116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000076 in 131,502 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000076 (0 hom., cov: 22)
• Consequence: ANKRD20A5P ENST00000581935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 1 publications found

Genes affected

ANKRD20A5P (HGNC:33833): (ankyrin repeat domain 20 family member A5, pseudogene)

ANKRD20A5P (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581935.5. 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
	ANKRD20A5P	NR_040113.1		n.501+1116T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD20A5P	ENST00000431648.8	TSL:6	n.203+1116T>A		intron	N/A
	ANKRD20A5P	ENST00000580995.2	TSL:5	n.316+1116T>A		intron	N/A
	ANKRD20A5P	ENST00000581181.6	TSL:3	n.643+1116T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000760 AC: 1 AN: 131502 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000155

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000760 AC: 1 AN: 131502 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 61760

African (AFR) AF: 0.00 AC: 0 AN: 34944

American (AMR) AF: 0.00 AC: 0 AN: 12372

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3368

East Asian (EAS) AF: 0.00 AC: 0 AN: 4724

South Asian (SAS) AF: 0.00 AC: 0 AN: 4416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3992

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.0000155 AC: 1 AN: 64724

Other (OTH) AF: 0.00 AC: 0 AN: 1810

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.095
PhyloP100		-0.24

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: rs554995;

hg19: chr18-14180712;