chr7-120114547-A-G

Position:

• chr7-120114547-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 0.0341 in 152,210 control chromosomes in the GnomAD database, including 115 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 0.034 (115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0616 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5185 AN: 152092 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0341 AC: 5192 AN: 152210 Hom.: 115 Cov.: 32 AF XY: 0.0344 AC XY: 2563 AN XY: 74432

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.0317

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0150 Hom.: 4

Bravo AF: 0.0327

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6979384; hg19: chr7-119754601;