rs6057110

chr20-10035559-C-Gchr20-10035559-C-T

Variant summary

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

The NM_022096.6(ANKEF1):c.-108-20C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,242 control chromosomes in the GnomAD database, including 3,342 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 0.20 (3342 hom., cov: 33)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: ANKEF1 NM_022096.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

ANKEF1 (HGNC:15803): (ankyrin repeat and EF-hand domain containing 1) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKEF1	NM_022096.6	c.-108-20C>G		intron_variant		ENST00000378392.6
SNAP25-AS1	NR_040710.1	n.500-8911G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKEF1	ENST00000378392.6	c.-108-20C>G		intron_variant		1	NM_022096.6	P1
SNAP25-AS1	ENST00000421143.6	n.235-8911G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30780 AN: 152108 Hom.: 3337 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.202 AC: 30819 AN: 152226 Hom.: 3342 Cov.: 33 AF XY: 0.199 AC XY: 14817 AN XY: 74422

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0206

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.210

Alfa AF: 0.197 Hom.: 403

Bravo AF: 0.199

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.2
Dann	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6057110; hg19: chr20-10016207;