rs17692896

Variant names:

• chr19-32598525-G-A
• rs17692896
• NM_032139.3:c.2920-147C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032139.3(ANKRD27):​c.2920-147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 699,950 control chromosomes in the GnomAD database, including 1,254 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 0.045 (231 hom., cov: 33)
  • Exomes 𝑓: 0.055 (1023 hom.)
• Consequence: ANKRD27 NM_032139.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 4 publications found

Genes affected

ANKRD27 (HGNC:25310): (ankyrin repeat domain 27) Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in endocytic recycling and negative regulation of SNARE complex assembly. Acts upstream of or within early endosome to late endosome transport. Located in endosome; lysosome; and plasma membrane. Implicated in eosinophilic esophagitis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032139.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD27	NM_032139.3	MANE Select	c.2920-147C>T		intron	N/A	NP_115515.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD27	ENST00000306065.9	TSL:1 MANE Select	c.2920-147C>T		intron	N/A	ENSP00000304292.3
	ANKRD27	ENST00000587667.1	TSL:2	n.389-147C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6868 AN: 152148 Hom.: 231 Cov.: 33

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0306

GnomAD4 exome AF: 0.0548 AC: 29989 AN: 547684 Hom.: 1023 AF XY: 0.0545 AC XY: 15719 AN XY: 288232

African (AFR) AF: 0.0111 AC: 171 AN: 15398

American (AMR) AF: 0.0193 AC: 548 AN: 28398

Ashkenazi Jewish (ASJ) AF: 0.0327 AC: 521 AN: 15910

East Asian (EAS) AF: 0.000125 AC: 4 AN: 31926

South Asian (SAS) AF: 0.0465 AC: 2533 AN: 54480

European-Finnish (FIN) AF: 0.0808 AC: 2708 AN: 33510

Middle Eastern (MID) AF: 0.0203 AC: 57 AN: 2806

European-Non Finnish (NFE) AF: 0.0652 AC: 21887 AN: 335600

Other (OTH) AF: 0.0526 AC: 1560 AN: 29656

GnomAD4 genome AF: 0.0451 AC: 6870 AN: 152266 Hom.: 231 Cov.: 33 AF XY: 0.0445 AC XY: 3311 AN XY: 74456

African (AFR) AF: 0.0110 AC: 456 AN: 41554

American (AMR) AF: 0.0279 AC: 427 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.0480 AC: 232 AN: 4832

European-Finnish (FIN) AF: 0.0841 AC: 891 AN: 10594

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0682 AC: 4639 AN: 68010

Other (OTH) AF: 0.0302 AC: 64 AN: 2116

Alfa AF: 0.0579 Hom.: 293

Bravo AF: 0.0388

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.50
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17692896; hg19: chr19-33089431;