7-30989018-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 XR_001745156.2(LOC105375222):​n.537-4155A>G variant causes a intron, non coding transcript 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: LOC105375222 XR_001745156.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

LOC105375222 (HGNC:):

GHRHR (HGNC:4266): (growth hormone releasing hormone receptor) This gene encodes a receptor for growth hormone-releasing hormone. Binding of this hormone to the receptor leads to synthesis and release of growth hormone. Mutations in this gene have been associated with isolated growth hormone deficiency (IGHD), also known as Dwarfism of Sindh, a disorder characterized by short stature. [provided by RefSeq, Jun 2010]

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	UniProt
LOC105375222	XR_001745156.2	n.537-4155A>G		intron_variant, non_coding_transcript_variant
LOC105375222	XR_001745155.2	n.537-4155A>G		intron_variant, non_coding_transcript_variant
LOC105375222	XR_927159.2	n.537-4155A>G		intron_variant, non_coding_transcript_variant
LOC105375222	XR_927160.2	n.537-4155A>G		intron_variant, non_coding_transcript_variant

Ensembl

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