7-30945961-G-A

Position:

• chr7-30945961-G-A

Variant summary

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

The variant allele was found at a frequency of 0.0756 in 151,848 control chromosomes in the GnomAD database, including 629 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 0.076 (629 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30945961G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GHRHR	ENST00000466427.1	n.284+7009G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11454 AN: 151730 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0756 AC: 11475 AN: 151848 Hom.: 629 Cov.: 32 AF XY: 0.0735 AC XY: 5454 AN XY: 74214

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0165

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0553 Hom.: 434

Bravo AF: 0.0821

Asia WGS AF: 0.0230 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10265249; hg19: chr7-30985576;