rs719235

Variant names:

• chr8-63039122-C-A
• rs719235
• ENST00000677327.1:n.286G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-63039122-C-A
• chr8-63039122-C-G
• chr8-63039122-C-T

Variant summary

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

The ENST00000679326.1(GGH):​n.-354G>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 0.229 in 207,172 control chromosomes in the GnomAD database, including 6,592 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 0.21 (4389 hom., cov: 33)
  • Exomes 𝑓: 0.27 (2203 hom.)
• Consequence: GGH ENST00000679326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 24 publications found

Genes affected

GGH (HGNC:4248): (gamma-glutamyl hydrolase) This gene catalyzes the hydrolysis of folylpoly-gamma-glutamates and antifolylpoly-gamma-glutamates by the removal of gamma-linked polyglutamates and glutamate. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679326.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GGH	ENST00000677327.1		n.286G>T		non_coding_transcript_exon	Exon 1 of 8
	GGH	ENST00000679326.1		n.-354G>T		non_coding_transcript_exon	Exon 1 of 10	ENSP00000504262.1	A0A7I2YQQ3
	GGH	ENST00000679326.1		n.-354G>T		5_prime_UTR	Exon 1 of 10	ENSP00000504262.1	A0A7I2YQQ3

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32479 AN: 152062 Hom.: 4382 Cov.: 33

Gnomad AFR AF: 0.0557

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.273 AC: 15005 AN: 54992 Hom.: 2203 Cov.: 0 AF XY: 0.276 AC XY: 7657 AN XY: 27792

African (AFR) AF: 0.0505 AC: 103 AN: 2038

American (AMR) AF: 0.198 AC: 292 AN: 1474

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 467 AN: 2212

East Asian (EAS) AF: 0.113 AC: 540 AN: 4790

South Asian (SAS) AF: 0.397 AC: 227 AN: 572

European-Finnish (FIN) AF: 0.364 AC: 1451 AN: 3986

Middle Eastern (MID) AF: 0.266 AC: 81 AN: 304

European-Non Finnish (NFE) AF: 0.303 AC: 10832 AN: 35740

Other (OTH) AF: 0.261 AC: 1012 AN: 3876

GnomAD4 genome AF: 0.213 AC: 32489 AN: 152180 Hom.: 4389 Cov.: 33 AF XY: 0.216 AC XY: 16056 AN XY: 74394

African (AFR) AF: 0.0555 AC: 2309 AN: 41580

American (AMR) AF: 0.190 AC: 2913 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.121 AC: 624 AN: 5148

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4826

European-Finnish (FIN) AF: 0.345 AC: 3658 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19827 AN: 67944

Other (OTH) AF: 0.220 AC: 465 AN: 2116

Alfa AF: 0.249 Hom.: 8522

Bravo AF: 0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		-0.15
PromoterAI		0.028	Neutral
Mutation Taster		=300/0	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: rs719235; hg19: chr8-63951681;