chr7-150980992-A-G

Position:

• chr7-150980992-A-G

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 0.361 in 152,006 control chromosomes in the GnomAD database, including 11,349 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 (11349 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150980992A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54800 AN: 151888 Hom.: 11316 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.361 AC: 54881 AN: 152006 Hom.: 11349 Cov.: 33 AF XY: 0.369 AC XY: 27386 AN XY: 74292

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.344

Alfa AF: 0.271 Hom.: 9343

Bravo AF: 0.378

Asia WGS AF: 0.586 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2373885; hg19: chr7-150678080;