5-140401510-A-C

Variant names:

• chr5-140401510-A-C
• rs17286683
• ENST00000507521.3:n.154T>G

Variant summary

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

The ENST00000507521.3(ANKHD1-DT):​n.154T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 158,782 control chromosomes in the GnomAD database, including 3,408 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 0.18 (3236 hom., cov: 32)
  • Exomes 𝑓: 0.21 (172 hom.)
• Consequence: ANKHD1-DT ENST00000507521.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 5 publications found

Genes affected

ANKHD1-DT (HGNC:55564): (ANKHD1 divergent transcript)

ENSG00000302458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507521.3. 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
	ANKHD1-DT	NR_186044.1		n.-109T>G		upstream_gene	N/A
	ANKHD1-DT	NR_186045.1		n.-109T>G		upstream_gene	N/A
	ANKHD1-DT	NR_186046.1		n.-109T>G		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKHD1-DT	ENST00000507521.3	TSL:2	n.154T>G		non_coding_transcript_exon	Exon 1 of 2
	ANKHD1-DT	ENST00000687631.3		n.183T>G		non_coding_transcript_exon	Exon 1 of 1
	ANKHD1-DT	ENST00000786872.1		n.197T>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27549 AN: 152140 Hom.: 3227 Cov.: 32

Gnomad AFR AF: 0.0441

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.215 AC: 1401 AN: 6524 Hom.: 172 AF XY: 0.223 AC XY: 794 AN XY: 3568

African (AFR) AF: 0.0714 AC: 17 AN: 238

American (AMR) AF: 0.183 AC: 33 AN: 180

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 59 AN: 270

East Asian (EAS) AF: 0.292 AC: 52 AN: 178

South Asian (SAS) AF: 0.239 AC: 200 AN: 836

European-Finnish (FIN) AF: 0.285 AC: 57 AN: 200

Middle Eastern (MID) AF: 0.125 AC: 2 AN: 16

European-Non Finnish (NFE) AF: 0.216 AC: 913 AN: 4224

Other (OTH) AF: 0.178 AC: 68 AN: 382

GnomAD4 genome AF: 0.181 AC: 27565 AN: 152258 Hom.: 3236 Cov.: 32 AF XY: 0.184 AC XY: 13674 AN XY: 74446

African (AFR) AF: 0.0439 AC: 1826 AN: 41576

American (AMR) AF: 0.211 AC: 3231 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1500 AN: 5176

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4830

European-Finnish (FIN) AF: 0.267 AC: 2825 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15720 AN: 68008

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.177 Hom.: 1156

Bravo AF: 0.169

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		-0.048
PromoterAI		-0.018	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17286683; hg19: chr5-139781095;