rs7610

Variant names:

• chr14-92934971-T-A
• rs7610
• NM_001275.4:c.*87T>A

Your query was ambiguous. Multiple possible variants found:

• chr14-92934971-T-A
• chr14-92934971-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001275.4(CHGA):​c.*87T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000292 in 1,026,200 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: CHGA NM_001275.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99
• Publications: 27 publications found

Genes affected

CHGA (HGNC:1929): (chromogranin A) The protein encoded by this gene is a member of the chromogranin/secretogranin family of neuroendocrine secretory proteins. It is found in secretory vesicles of neurons and endocrine cells. This gene product is a precursor to three biologically active peptides; vasostatin, pancreastatin, and parastatin. These peptides act as autocrine or paracrine negative modulators of the neuroendocrine system. Two other peptides, catestatin and chromofungin, have antimicrobial activity and antifungal activity, respectively. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHGA	NM_001275.4	c.*87T>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000216492.10	NP_001266.1
CHGA	NM_001301690.2	c.*87T>A		3_prime_UTR_variant	Exon 7 of 7		NP_001288619.1
CHGA	XM_011536370.3	c.*87T>A		3_prime_UTR_variant	Exon 9 of 9		XP_011534672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHGA	ENST00000216492.10	c.*87T>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_001275.4	ENSP00000216492.5
CHGA	ENST00000334654.4	c.*87T>A		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000334023.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000292 AC: 3 AN: 1026200 Hom.: 0 Cov.: 13 AF XY: 0.00000586 AC XY: 3 AN XY: 511516

African (AFR) AF: 0.00 AC: 0 AN: 20924

American (AMR) AF: 0.00 AC: 0 AN: 16964

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19308

East Asian (EAS) AF: 0.00 AC: 0 AN: 30012

South Asian (SAS) AF: 0.0000175 AC: 1 AN: 57296

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45450

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3478

European-Non Finnish (NFE) AF: 0.00000254 AC: 2 AN: 787922

Other (OTH) AF: 0.00 AC: 0 AN: 44846

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.024
DANN	Benign	0.43
PhyloP100		-4.0

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: rs7610; hg19: chr14-93401316;