chr20-58221728-G-C

Variant names:

• chr20-58221728-G-C
• rs4811971
• NM_001304369.2:c.562-225C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001304369.2(ANKRD60):​c.562-225C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ANKRD60 NM_001304369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

ANKRD60 (HGNC:16217): (ankyrin repeat domain 60)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD60	NM_001304369.2	c.562-225C>G		intron_variant	Intron 2 of 3	ENST00000457363.2	NP_001291298.1
ANKRD60	XM_047439902.1	c.562-225C>G		intron_variant	Intron 2 of 3		XP_047295858.1
ANKRD60	XM_047439903.1	c.562-225C>G		intron_variant	Intron 2 of 3		XP_047295859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD60	ENST00000457363.2	c.562-225C>G		intron_variant	Intron 2 of 3	5	NM_001304369.2	ENSP00000396747.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0060
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811971; hg19: chr20-56796784;