rs6057110

Variant names:

• chr20-10035559-C-G
• rs6057110
• NM_022096.6:c.-108-20C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-10035559-C-G
• chr20-10035559-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ANKEF1	NM_022096.6	c.-108-20C>G		intron_variant	Intron 1 of 10	ENST00000378392.6	NP_071379.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKEF1	ENST00000378392.6	c.-108-20C>G		intron_variant	Intron 1 of 10	1	NM_022096.6	ENSP00000367644.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 2 AN: 8

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.269 AC: 11161 AN: 41514

American (AMR) AF: 0.142 AC: 2174 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.0206 AC: 107 AN: 5186

South Asian (SAS) AF: 0.168 AC: 811 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2037 AN: 10594

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13185 AN: 68012

Other (OTH) AF: 0.210 AC: 443 AN: 2114

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
PhyloP100		-0.021
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6057110; hg19: chr20-10016207;