rs4811971

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-58221728-G-A
• chr20-58221728-G-C

Variant summary

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

The NM_001304369.2(ANKRD60):​c.562-225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,958 control chromosomes in the GnomAD database, including 31,274 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 0.63 (31274 hom., 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD60	NM_001304369.2	c.562-225C>T		intron_variant	Intron 2 of 3	ENST00000457363.2	NP_001291298.1
ANKRD60	XM_047439902.1	c.562-225C>T		intron_variant	Intron 2 of 3		XP_047295858.1
ANKRD60	XM_047439903.1	c.562-225C>T		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>T		intron_variant	Intron 2 of 3	5	NM_001304369.2	ENSP00000396747.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96146 AN: 151840 Hom.: 31266 Cov.: 30

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.633 AC: 96188 AN: 151958 Hom.: 31274 Cov.: 30 AF XY: 0.636 AC XY: 47202 AN XY: 74248

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.682

Alfa AF: 0.687 Hom.: 43243

Bravo AF: 0.631

Asia WGS AF: 0.609 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.70

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;