rs12053254

chr2-189742427-T-C

Variant summary

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

The NM_001378068.1(ANKAR):c.3811-848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,170 control chromosomes in the GnomAD database, including 623 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 0.080 (623 hom., cov: 32)
• Consequence: ANKAR NM_001378068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

Genes affected

ANKAR (HGNC:26350): (ankyrin and armadillo repeat containing) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKAR	NM_001378068.1	c.3811-848T>C		intron_variant		ENST00000684021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKAR	ENST00000684021.1	c.3811-848T>C		intron_variant			NM_001378068.1	P1

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12236 AN: 152052 Hom.: 623 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0804 AC: 12240 AN: 152170 Hom.: 623 Cov.: 32 AF XY: 0.0810 AC XY: 6027 AN XY: 74390

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0393

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.0477

Gnomad4 OTH AF: 0.0648

Alfa AF: 0.0553 Hom.: 276

Bravo AF: 0.0862

Asia WGS AF: 0.0770 AC: 268 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	4.1
Dann	Benign	0.83

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: rs12053254; hg19: chr2-190607153;