chr7-30989018-A-G

Position:

• chr7-30989018-A-G

Variant summary

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

The ENST00000473133.1(GHRHR):​n.280-4155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,104 control chromosomes in the GnomAD database, including 13,422 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 0.36 (13422 hom., cov: 32)
• Consequence: GHRHR ENST00000473133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

GHRHR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375222	XR_001745155.2	n.537-4155A>G		intron_variant
LOC105375222	XR_001745156.2	n.537-4155A>G		intron_variant
LOC105375222	XR_927159.2	n.537-4155A>G		intron_variant
LOC105375222	XR_927160.2	n.537-4155A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHRHR	ENST00000473133.1	n.280-4155A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54186 AN: 151986 Hom.: 13400 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.357 AC: 54245 AN: 152104 Hom.: 13422 Cov.: 32 AF XY: 0.350 AC XY: 26045 AN XY: 74360

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.334

Alfa AF: 0.271 Hom.: 1550

Bravo AF: 0.375

Asia WGS AF: 0.284 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11760522; hg19: chr7-31028633;