chr7-145321424-A-G

Position:

• chr7-145321424-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 0.397 in 152,000 control chromosomes in the GnomAD database, including 13,010 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 0.40 (13010 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60390 AN: 151882 Hom.: 13013 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60405 AN: 152000 Hom.: 13010 Cov.: 33 AF XY: 0.405 AC XY: 30102 AN XY: 74282

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.396

Alfa AF: 0.418 Hom.: 2318

Bravo AF: 0.390

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.27
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996343; hg19: chr7-145018517;