rs34018897

Variant names:

• chr16-67483735-C-T
• rs34018897
• ENST00000602596.1:n.137-375C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The ENST00000602596.1(ATP6V0D1-DT):​n.137-375C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 177,134 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0019 (0 hom.)
• Consequence: ATP6V0D1-DT ENST00000602596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

Genes affected

ATP6V0D1-DT (HGNC:55268): (ATP6V0D1 divergent transcript)

AGRP (HGNC:330): (agouti related neuropeptide) This gene encodes an antagonist of the melanocortin-3 and melanocortin-4 receptor. It appears to regulate hypothalamic control of feeding behavior via melanocortin receptor and/or intracellular calcium regulation, and thus plays a role in weight homeostasis. Mutations in this gene have been associated with late on-set obesity. [provided by RefSeq, Dec 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGRP	NM_001138.2	c.-222G>A		upstream_gene_variant		ENST00000290953.3	NP_001129.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGRP	ENST00000290953.3	c.-222G>A		upstream_gene_variant		1	NM_001138.2	ENSP00000290953.3

Frequencies

GnomAD3 genomes AF: 0.00113 AC: 172 AN: 152160 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000338

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000786

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00157

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.00193 AC: 48 AN: 24856 Hom.: 0 Cov.: 0 AF XY: 0.00193 AC XY: 24 AN XY: 12422

African (AFR) AF: 0.00198 AC: 2 AN: 1012

American (AMR) AF: 0.00360 AC: 3 AN: 834

Ashkenazi Jewish (ASJ) AF: 0.00181 AC: 2 AN: 1102

East Asian (EAS) AF: 0.00 AC: 0 AN: 1560

South Asian (SAS) AF: 0.00313 AC: 1 AN: 320

European-Finnish (FIN) AF: 0.000782 AC: 1 AN: 1278

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 152

European-Non Finnish (NFE) AF: 0.00219 AC: 37 AN: 16882

Other (OTH) AF: 0.00117 AC: 2 AN: 1716

GnomAD4 genome AF: 0.00113 AC: 172 AN: 152278 Hom.: 0 Cov.: 33 AF XY: 0.00118 AC XY: 88 AN XY: 74462

African (AFR) AF: 0.000337 AC: 14 AN: 41550

American (AMR) AF: 0.000785 AC: 12 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4830

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00157 AC: 107 AN: 68034

Other (OTH) AF: 0.00142 AC: 3 AN: 2114

Alfa AF: 0.00175 Hom.: 0

Bravo AF: 0.00116

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		-0.080
PromoterAI		0.0076	Neutral
Mutation Taster		=285/15	polymorphism

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: rs34018897; hg19: chr16-67517638;