rs4459610

Positions:

• chr17-63507359-A-T

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.2145A>T 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 0.54 in 398,798 control chromosomes in the GnomAD database, including 60,001 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 0.54 (22985 hom., cov: 32)
  • Exomes 𝑓: 0.54 (37016 hom.)
• Consequence: ENSG00000264813 ENST00000577647.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACE3P		n.63507359A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000264813	ENST00000577647.2	n.2145A>T		non_coding_transcript_exon_variant	15/31	2		ENSP00000464149.1
ACE3P	ENST00000423435.2	n.58-205A>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82666 AN: 151888 Hom.: 22965 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.580

GnomAD3 exomes AF: 0.552 AC: 4845 AN: 8782 Hom.: 1341 AF XY: 0.559 AC XY: 2358 AN XY: 4216

Gnomad AFR exome AF: 0.535

Gnomad AMR exome AF: 0.424

Gnomad ASJ exome AF: 0.707

Gnomad EAS exome AF: 0.236

Gnomad SAS exome AF: 0.349

Gnomad FIN exome AF: 0.486

Gnomad NFE exome AF: 0.572

Gnomad OTH exome AF: 0.592

GnomAD4 exome AF: 0.537 AC: 132457 AN: 246792 Hom.: 37016 Cov.: 0 AF XY: 0.541 AC XY: 67622 AN XY: 125090

Gnomad4 AFR exome AF: 0.581

Gnomad4 AMR exome AF: 0.437

Gnomad4 ASJ exome AF: 0.680

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.496

Gnomad4 NFE exome AF: 0.576

Gnomad4 OTH exome AF: 0.542

GnomAD4 genome AF: 0.544 AC: 82721 AN: 152006 Hom.: 22985 Cov.: 32 AF XY: 0.534 AC XY: 39639 AN XY: 74288

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.576

Alfa AF: 0.566 Hom.: 3047

Bravo AF: 0.544

Asia WGS AF: 0.331 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.75

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: rs4459610; hg19: chr17-61584720;